The crystal structure of vanthoffite {hexasodium magnesium tetrakis[sulfate(VI)]}, Na6Mg(SO4)4, was solved in the year 1964 on a synthetic sample [Fischer & Hellner (1964). Acta Cryst. 17, 1613]. Here we report a redetermination of its crystal structure on a mineral sample with improved precision. It was refined in the space group P21/c from a crystal originating from Surtsey, Iceland. The unique Mg (site symmetry overline{1}) and the two S atoms are in usual, only slightly distorted octahedral and tetrahedral coordinations, respectively. The three independent Na atoms are in a distorted octahedral coordination (1×) and distorted 7-coordinations intermediate between a `split octahedron' and a pentagonal bipyramid (2×). [MgO6] coordination polyhedra interchange with one half of the sulfate tetrahedra in <011> chains forming a (100) meshed layer, with dimers formed by edge-sharing [NaO7] polyhedra filling the interchain spaces. The other [NaO7] polyhedra are organized in a parallel layer formed by [010] and [001] chains united through edge sharing and bonds to the remaining half of sulfate groups and to [NaO6] octahedra. The two types of layers interconnect through tight bonding, which explains the lack of morphological characteristics typical of layered structures.

The new copper(II) complex, namely, di-μ-chlorido-bis{chlorido[methyl(pyridin-2-ylmethylidene)amine-κ2N,N']copper(II)}, [Cu2Cl4(C7H8N2)2], (I), with the ligand 2-pyridylmethyl-N-methylimine (L, a product of Schiff base condensation between methylamine and 2-pyridinecarbaldehyde) is built of discrete centrosymmetric dimers. The coordination about the CuII ion can be described as distorted square pyramidal. The base of the pyramid consists of two nitrogen atoms from the bidentate chelate L [Cu—N = 2.0241 (9), 2.0374 (8) Å] and two chlorine atoms [Cu—Cl = 2.2500 (3), 2.2835 (3) Å]. The apical position is occupied by another Cl atom with the apical bond being significantly elongated at 2.6112 (3) Å. The trans angles of the base are 155.16 (3) and 173.79 (2)°. The Cu...Cu separation in the dimer is 3.4346 (3) Å. In the crystal structure, the loosely packed dimers are arranged in stacks propagating along the a axis. The X-band polycrystalline 77 K EPR spectrum of (I) demonstrates a typical axial pattern characteristic of mononuclear CuII complexes. Compound (I) is redox active and shows a cyclic voltammetric response with E1/2 = −0.037 V versus silver–silver chloride electrode (SSCE) assignable to the reduction peak of CuII/CuI in methanol as solvent.

In the title compound, C17H27NO2, the piperidine ring has a chair conformation and is positioned normal to the benzene ring. In the crystal, molecules are linked by C—H...O hydrogen bonds, forming chains propagating along the c-axis direction.

The asymmetric unit of the title compound, C17H14N2O, contains two independent molecules each consisting of perimidine and phenol units. The tricyclic perimidine units contain naphthalene ring systems and non-planar C4N2 rings adopting envelope conformations with the C atoms of the NCN groups hinged by 44.11 (7) and 48.50 (6)° with respect to the best planes of the other five atoms. Intramolecular O—H...N hydrogen bonds may help to consolidate the molecular conformations. The two independent molecules are linked through an N—H...O hydrogen bond. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H...H (52.9%) and H...C/C...H (39.5%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. Density functional theory (DFT) optimized structures at the B3LYP/ 6–311 G(d,p) level are compared with the experimentally determined molecular structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap.

The cationic complex in the title compound, [Ir(C9H7N2)2(C12H8N2)]PF6, comprises two phenylpyrazole (ppz) cyclometallating ligands and one 1,10-phenanthroline (phen) ancillary ligand. The asymmetric unit consists of one [Ir(ppz)2(phen)]+ cation and one [PF6]− counter-ion. The central IrIII ion is six-coordinated by two N atoms and two C atoms from the two ppz ligands as well as by two N atoms from the phen ligand within a distorted octahedral C2N4 coordination set. In the crystal structure, the [Ir(ppz)2(phen)]+ cations and PF6− counter-ions are connected with each other through weak intermolecular C—H...F hydrogen bonds. Additional C—H...π interactions between the rings of neighbouring cations consolidate the three-dimensional network. Electron density associated with additional disordered solvent molecules inside cavities of the structure was removed with the SQUEEZE procedure in PLATON [Spek (2015). Acta Cryst. C71, 9–18]. The given chemical formula and other crystal data do not take into account the unknown solvent molecule(s). The title compound has a different space-group symmetry (C2/c) from its solvatomorph (P21/c) comprising 1.5CH2Cl2 solvent molecules per ion pair.

The title compound, C14H16, exhibits exceptionally weak intermolecular C—H...π hydrogen bonding of the ethynyl groups, with the corresponding H...π separations [2.91 (2) and 3.12 (2) Å] exceeding normal vdW distances. This bonding complements distal contacts of the CH (aliphatic)...π type [H...π = 3.12 (2)–3.14 (2) Å] to sustain supramolecular layers. Hirshfeld surface analysis of the title compound suggests a relatively limited significance of the C...H/H...C contacts to the crystal packing (24.6%) and a major contribution from H...H contacts accounting 74.9% to the entire surface.

In the title compound, C16H14Cl2FN3, the dihedral angle between the two aromatic rings is 64.12 (14)°. The crystal structure is stabilized by a short Cl...H contact, C—Cl...π and van der Waals interactions. The Hirshfeld surface analysis and two-dimensional fingerprint plots show that H...H (33.3%), Cl...H/H...Cl (22.9%) and C...H/H...C (15.5%) interactions are the most important contributors towards the crystal packing.

This work considers the scaling properties characterizing the hyperuniformity (or anti-hyperuniformity) of long-wavelength fluctuations in a broad class of one-dimensional substitution tilings. A simple argument is presented which predicts the exponent α governing the scaling of Fourier intensities at small wavenumbers, tilings with α > 0 being hyperuniform, and numerical computations confirm that the predictions are accurate for quasiperiodic tilings, tilings with singular continuous spectra and limit-periodic tilings. Quasiperiodic or singular continuous cases can be constructed with α arbitrarily close to any given value between −1 and 3. Limit-periodic tilings can be constructed with α between −1 and 1 or with Fourier intensities that approach zero faster than any power law.

Diffuse scattering is a rich source of information about disorder in crystalline materials, which can be modelled using atomistic techniques such as Monte Carlo and molecular dynamics simulations. Modern X-ray and neutron scattering instruments can rapidly measure large volumes of diffuse-scattering data. Unfortunately, current algorithms for atomistic diffuse-scattering calculations are too slow to model large data sets completely, because the fast Fourier transform (FFT) algorithm has long been considered unsuitable for such calculations [Butler & Welberry (1992). J. Appl. Cryst. 25, 391–399]. Here, a new approach is presented for ultrafast calculation of atomistic diffuse-scattering patterns. It is shown that the FFT can actually be used to perform such calculations rapidly, and that a fast method based on sampling theory can be used to reduce high-frequency noise in the calculations. These algorithms are benchmarked using realistic examples of compositional, magnetic and displacive disorder. They accelerate the calculations by a factor of at least 102, making refinement of atomistic models to large diffuse-scattering volumes practical.

To date X-ray protein crystallography is the most successful technique available for the determination of high-resolution 3D structures of biological molecules and their complexes. In X-ray protein crystallography the structure of a protein is refined against the set of observed Bragg reflections from a protein crystal. The resolution of the refined protein structure is limited by the highest angle at which Bragg reflections can be observed. In addition, the Bragg reflections alone are typically insufficient (by a factor of two) to determine the structure ab initio, and so prior information is required. Crystals formed from an imperfect packing of the protein molecules may also exhibit continuous diffraction between and beyond these Bragg reflections. When this is due to random displacements of the molecules from each crystal lattice site, the continuous diffraction provides the necessary information to determine the protein structure without prior knowledge, to a resolution that is not limited by the angular extent of the observed Bragg reflections but instead by that of the diffraction as a whole. This article presents an iterative projection algorithm that simultaneously uses the continuous diffraction as well as the Bragg reflections for the determination of protein structures. The viability of this method is demonstrated on simulated crystal diffraction.

One of the essential components of molecular electronic circuits are switching elements that are stable in two different states and can ideally be switched on and off many times. Here, distinct buckminsterfullerenes within a self-assembled monolayer, forming a two-dimensional dodecagonal quasicrystal on a Pt-terminated Pt3Ti(111) surface, are identified to form well separated molecular rotational switching elements. Employing scanning tunneling microscopy, the molecular-orbital appearance of the fullerenes in the quasicrystalline monolayer is resolved. Thus, fullerenes adsorbed on the 36 vertex configuration are identified to exhibit a distinctly increased mobility. In addition, this finding is verified by differential conductance measurements. The rotation of these mobile fullerenes can be triggered frequently by applied voltage pulses, while keeping the neighboring molecules immobile. An extensive analysis reveals that crystallographic and energetic constraints at the molecule/metal interface induce an inequality of the local potentials for the 36 and 32.4.3.4 vertex sites and this accounts for the switching ability of fullerenes on the 36 vertex sites. Consequently, a local area of the 8/3 approximant in the two-dimensional fullerene quasicrystal consists of single rotational switching fullerenes embedded in a matrix of inert molecules. Furthermore, it is deduced that optimization of the intermolecular interactions between neighboring fullerenes hinders the realization of translational periodicity in the fullerene monolayer on the Pt-terminated Pt3Ti(111) surface.

A new aspherical scattering factor formalism has been implemented in the crystallographic least-squares refinement program SHELXL. The formalism relies on Gaussian functions and can optionally complement the independent atom model to take into account the deformation of electron-density distribution due to chemical bonding and lone pairs. Asphericity contributions were derived from the electron density obtained from quantum-chemical density functional theory computations of suitable model compounds that contain particular chemical environments, as defined by the invariom formalism. Thanks to a new algorithm, invariom assignment for refinement in SHELXL is automated. A suitable parameterization for each chemical environment within the new model was achieved by metaheuristics. Figures of merit, precision and accuracy of crystallographic least-squares refinements improve significantly upon using the new model.

The methods for X-ray crystal orientation are rapidly evolving towards versatility, fewer goniometry measurements, automation, high accuracy and precision. One method that attracts a lot of attention is energy-dispersive X-ray diffraction (EDXRD) which is based on detecting reflections from crystallographic planes in a crystal at fixed angles of a parallel polychromatic X-ray incident beam. In theory, an EDXRD peak can move in a diffraction pattern as a function of a crystallographic plane d-spacing and its orientation relative to a fixed direction in space can change also. This is equivalent to the possibility of measuring the orientation of single crystals. The article provides a modeling for the EDXRD method whose main feature is the nonmoving crystal in the sense of traditional goniometry where the angle measurements of diffracting planes are a must. The article defines the equation of orientation for the method and shows the derivation in great detail. It is shown that the exact solutions of the equations can be obtained using the generalized reduced gradient method, a mathematical subroutine that is implemented in Excel software. The significance and scientific impact of the work are discussed along with the validated tested results.

It is shown how to reconstruct the stacking sequence from the pairwise correlation functions between layers in close-packed structures. First, of theoretical interest, the analytical formulation and solution of the problem are presented when the exact pairwise correlation counts are known. In the second part, the practical problem is approached. A simulated annealing procedure is developed to solve the problem using as initial guess approximate solutions from previous treatments. The robustness of the procedure is tested with synthetic data, followed by an experimental example. The developed approach performs robustly over different synthetic and experimental data, comparing favorably with the reported methods.

Compared with X-rays, electron diffraction faces a crucial challenge: dynamical electron scattering compromises structure solution and its effects can only be modelled in specific cases. Dynamical scattering can be reduced experimentally by decreasing crystal size but not without a penalty, as it also reduces the overall diffracted intensity. In this article it is shown that nanometre-sized crystals from organic pharmaceuticals allow positional refinement of the hydrogen atoms, even whilst ignoring the effects of dynamical scattering during refinement. To boost the very weak diffraction data, a highly sensitive hybrid pixel detector was employed. A general likelihood-based computational approach was also introduced for further reducing the adverse effects of dynamic scattering, which significantly improved model accuracy, even for protein crystal data at substantially lower resolution.

In this article, a framework is presented that allows the systematic derivation of planar edge-to-edge k-isocoronal tilings from tile-s-transitive tilings, s ≤ k. A tiling {cal T} is k-isocoronal if its vertex coronae form k orbits or k transitivity classes under the action of its symmetry group. The vertex corona of a vertex x of {cal T} is used to refer to the tiles that are incident to x. The k-isocoronal tilings include the vertex-k-transitive tilings (k-isogonal) and k-uniform tilings. In a vertex-k-transitive tiling, the vertices form k transitivity classes under its symmetry group. If this tiling consists of regular polygons then it is k-uniform. This article also presents the classification of isocoronal tilings in the Euclidean plane.

The structural and nonlinear optical properties of a new anilinium hybrid crystal of chemical formula (C6H7NCl+·NO3−)3 have been investigated. The crystal structure was determined from single-crystal X-ray diffraction measurements performed at a temperature of 100 K which show that the compound crystallizes in a noncentrosymmetric space group (Pna21). The structural analysis was coupled with Hirshfeld surface analysis to evaluate the contribution of the different intermolecular interactions to the formation of supramolecular assemblies in the solid state that exhibit nonlinear optical features. This analysis reveals that the studied compound is characterized by a three-dimensional network of hydrogen bonds and the main contributions are provided by the O...H, C...H, H...H and Cl...H interactions, which alone represent ∼85% of the total contributions to the Hirshfeld surfaces. It is noteworthy that the halogen...H contributions are quite comparable with those of the H...H contacts. The nonlinear optical properties were investigated by nonlinear diffuse femtosecond-pulse reflectometry and the obtained results were compared with those of the reference material LiNbO3. The hybrid crystals exhibit notable second (SHG) and third (THG) harmonic generation which confirms its polarity is generated by the different intermolecular interactions. These measurements also highlight that the THG signal of the new anilinium compound normalized to its SHG counterpart is more pronounced than for LiNbO3.

The unit-cell reduction described by Selling and used by Delone (whose early publications were under the spelling Delaunay) is explained in a simple form. The transformations needed to implement the reduction are listed. The simplicity of this reduction contrasts with the complexity of Niggli reduction.

An elementary method is described for finding the coordination sequences for a tiling, based on coloring the underlying graph. The first application is to the two kinds of vertices (tetravalent and trivalent) in the Cairo (or dual-32.4.3.4) tiling. The coordination sequence for a tetravalent vertex turns out, surprisingly, to be 1, 4, 8, 12, 16, …, the same as for a vertex in the familiar square (or 44) tiling. The authors thought that such a simple fact should have a simple proof, and this article is the result. The method is also used to obtain coordination sequences for the 32.4.3.4, 3.4.6.4, 4.82, 3.122 and 34.6 uniform tilings, and the snub-632 tiling. In several cases the results provide proofs for previously conjectured formulas.

The development of antiviral strategies requires a clear understanding of the principles that control the protein arrangements in viral shells. Considered here are those capsids that violate the paradigmatic Caspar and Klug (CK) model, and it is shown that the important structural features of such anomalous shells from the Picobirnaviridae, Flaviviridae and Leviviridae families can be revealed by models in the form of spherical icosahedral packings of equivalent rhombic structural units (SUs). These SUs are composed of protein dimers forming the investigated capsids which, as shown here, are based on the rhombic triacontahedron (RT) geometry. How to modify the original CK approach in order to make it compatible with the considered rhombic tessellations of a sphere is also discussed. Analogies between capsids self-assembled from dimers and trimers are demonstrated. This analysis reveals the principles controlling the localization of receptor proteins (which recognize the host cell) on the capsid surface.

The standard method of joint probability distribution functions, so crucial for the development of direct methods, has been revisited and updated. It consists of three steps: identification of the reflections which may contribute to the estimation of a given structure invariant or seminvariant, calculation of the corresponding joint probability distribution, and derivation of the conditional distribution of the invariant or seminvariant phase given the values of some diffracted amplitudes. In this article the conditional distributions are derived directly without passing through the second step. A good feature of direct methods is that they may work in the absence of any prior information: that is also their weakness. Different types of prior information have been taken into consideration: interatomic distances, interatomic vectors, Patterson peaks, structural model. The method of directly deriving the conditional distributions has been applied to those cases. Some new formulas have been obtained estimating two-, three- and four-phase invariants. Special attention has been dedicated to the practical aspects of the new formulas, in order to simplify their possible use in direct phasing procedures.

This work presents a technique for extracting the detailed shape of peaks with extended, overlapping tails in an X-ray powder diffraction pattern. The application discussed here concerns crystallite size broadening, though the technique can be applied to spectra of any origin and without regard to how the profiles are to be subsequently analyzed. Historically, the extraction of profile shapes has been difficult due to the complexity of determining the background under the peak, resulting in an offset of the low-frequency components of the Fourier transform of the peak known as the `hook' problem. The use of a carefully considered statistical weighting function in a non-linear least-squares fit, followed by summing the residuals from such a fit with the fit itself, allows one to extract the full shape of an isolated peak, without contributions from either the background or adjacent peaks. The extracted shape, consisting of the fit function recombined with the residuals, is not dependent on any specific shape model. The application of this to analysis of microstructure is performed independently of global parametric models, which would reduce the number of refined parameters; therefore the technique requires high-quality data to produce results of interest. The effectiveness of the technique is demonstrated by extraction of Fourier transforms of peaks from two sets of size-broadened materials with two differing pieces of equipment.

The report of the Executive Committee for 2017 is presented.

If searches from a browser's address bar and possibly search engines are being redirected through the site https://srchus.xyz.com/, then you most likely have a browser extension or addon installed that is causing these redirects. Some extension will cause all of the searches from your browser's address bar to redirect through https://srchus.xyz.com/, which redirects to https://vitosc.xyz/.

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If you see a web site that states "Press <> to watch the video" and then prompts you to allow browser notifications, do not click on the allow button. These sites are just trying to trick you into subscribing to their browser notifications so that they can send notification spam directly to your desktop.

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The Windows Defender Browser Protection tech support scam is a fake web site alert that states that Windows Defender Browser Extension detected someone to hack your bank account.

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Full System Care PUP is a potentially unwanted program that states it scans Windows for Malware/Pup Threats, ways to Enhance System Performance, System/User Software Related issues, and Startup/Uninstall and User Items. When Full System Care scans a computer it will list a variety of detected issues, but state that you need to first purchase a license before you can fix them. My concern is that many of the issues that it detects are not what I feel would cause a problem on a computer.

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The number of new X-ray crystallography-based submissions to the Protein Data Bank appears to be at the beginning of a decline, perhaps signalling an end to the era of the dominance of X-ray crystallography within structural biology. This letter, from the viewpoint of a young structural biologist, applies the Copernican method to the life expectancy of crystallography and asks whether the technique is still the mainstay of structural biology. A study of the rate of Protein Data Bank depositions allows a more nuanced analysis of the fortunes of macromolecular X-ray crystallography and shows that cryo-electron microscopy might now be outcompeting crystallography for new labour and talent, perhaps heralding a change in the landscape of the field.

Leucocyte common antigen-related protein (LAR) is a post-synaptic type I transmembrane receptor protein that is important for neuronal functionality and is genetically coupled to neuronal disorders such as attention deficit hyperactivity disorder (ADHD). To understand the molecular function of LAR, structural and biochemical studies of protein fragments derived from the ectodomain of human LAR have been performed. The crystal structure of a fragment encompassing the first four FNIII domains (LARFN1–4) showed a characteristic L shape. SAXS data suggested limited flexibility within LARFN1–4, while rigid-body refinement of the SAXS data using the X-ray-derived atomic model showed a smaller angle between the domains defining the L shape compared with the crystal structure. The capabilities of the individual LAR fragments to interact with heparin was examined using microscale thermophoresis and heparin-affinity chromatography. The results showed that the three N-terminal immunoglobulin domains (LARIg1–3) and the four C-terminal FNIII domains (LARFN5–8) both bound heparin, while LARFN1–4 did not. The low-molecular-weight heparin drug Innohep induced a shift in hydrodynamic volume as assessed by size-exclusion chromatography of LARIg1–3 and LARFN5–8, while the chemically defined pentameric heparin drug Arixtra did not. Together, the presented results suggest the presence of an additional heparin-binding site in human LAR.

Mycoplasma hyopneumoniae is a prokaryotic pathogen that colonizes the respiratory ciliated epithelial cells in swine. Infected animals suffer respiratory lesions, causing major economic losses in the porcine industry. Characterization of the immunodominant membrane-associated proteins from M. hyopneumoniae may be instrumental in the development of new therapeutic approaches. Here, the crystal structure of P46, one of the main surface-antigen proteins, from M. hyopneumoniae is presented and shows N- and C-terminal α/β domains connected by a hinge. The structures solved in this work include a ligand-free open form of P46 (3.1 Å resolution) and two ligand-bound structures of P46 with maltose (2.5 Å resolution) and xylose (3.5 Å resolution) in open and closed conformations, respectively. The ligand-binding site is buried in the cleft between the domains at the hinge region. The two domains of P46 can rotate with respect to each other, giving open or closed alternative conformations. In agreement with this structural information, sequence analyses show similarities to substrate-binding members of the ABC transporter superfamily, with P46 facing the extracellular side as a functional subunit. In the structure with xylose, P46 was also bound to a high-affinity (Kd = 29 nM) Fab fragment from a monoclonal antibody, allowing the characterization of a structural epitope in P46 that exclusively involves residues from the C-terminal domain. The Fab structure in the complex with P46 shows only small conformational rearrangements in the six complementarity-determining regions (CDRs) with respect to the unbound Fab (the structure of which is also determined in this work at 1.95 Å resolution). The structural information that is now available should contribute to a better understanding of sugar nutrient intake by M. hyopneumoniae. This information will also allow the design of protocols and strategies for the generation of new vaccines against this important swine pathogen.

The bond-valence method has been used for valence calculations of FeMo/V cofactors in FeMo/V proteins using 51 crystallographic data sets of FeMo/V proteins from the Protein Data Bank. The calculations show molybdenum(III) to be present in MoFe7S9C(Cys)(HHis)[R-(H)homocit] (where H4homocit is homocitric acid, HCys is cysteine and HHis is histidine) in FeMo cofactors, while vanadium(III) with a more reduced iron complement is obtained for FeV cofactors. Using an error analysis of the calculated valences, it was found that in FeMo cofactors Fe1, Fe6 and Fe7 can be unambiguously assigned as iron(III), while Fe2, Fe3, Fe4 and Fe5 show different degrees of mixed valences for the individual Fe atoms. For the FeV cofactors in PDB entry 5n6y, Fe4, Fe5 and Fe6 correspond to iron(II), iron(II) and iron(III), respectively, while Fe1, Fe2, Fe3 and Fe7 exhibit strongly mixed valences. Special situations such as CO-bound and selenium-substituted FeMo cofactors and O(N)H-bridged FeV cofactors are also discussed and suggest rearrangement of the electron configuration on the substitution of the bridging S atoms.

Death-associated protein kinase 1 (DAPK1) is a serine/threonine protein kinase that regulates apoptosis and autophagy. DAPK1 is considered to be a therapeutic target for amyloid-β deposition, endometrial adenocarcinomas and acute ischemic stroke. Here, the potent inhibitory activity of the natural anthraquinone purpurin against DAPK1 phosphorylation is shown. Thermodynamic analysis revealed that while the binding affinity of purpurin is similar to that of CPR005231, which is a DAPK1 inhibitor with an imidazopyridazine moiety, the binding of purpurin was more enthalpically favorable. In addition, the inhibition potencies were correlated with the enthalpic changes but not with the binding affinities. Crystallographic analysis of the DAPK1–purpurin complex revealed that the formation of a hydrogen-bond network is likely to contribute to the favorable enthalpic changes and that stabilization of the glycine-rich loop may cause less favorable entropic changes. The present findings indicate that purpurin may be a good lead compound for the discovery of inhibitors of DAPK1, and the observation of enthalpic changes could provide important clues for drug development.

Pullulanase (EC 3.2.1.41) is a well known starch-debranching enzyme that catalyzes the cleavage of α-1,6-glycosidic linkages in α-glucans such as starch and pullulan. Crystal structures of a type I pullulanase from Paenibacillus barengoltzii (PbPulA) and of PbPulA in complex with maltopentaose (G5), maltohexaose (G6)/α-cyclodextrin (α-CD) and β-cyclodextrin (β-CD) were determined in order to better understand substrate binding to this enzyme. PbPulA belongs to glycoside hydrolase (GH) family 13 subfamily 14 and is composed of three domains (CBM48, A and C). Three carbohydrate-binding sites identified in PbPulA were located in CBM48, near the active site and in domain C, respectively. The binding site in CBM48 was specific for β-CD, while that in domain C has not been reported for other pullulanases. The domain C binding site had higher affinity for α-CD than for G6; a small motif (FGGEH) seemed to be one of the major determinants for carbohydrate binding in this domain. Structure-based mutations of several surface-exposed aromatic residues in CBM48 and domain C had a debilitating effect on the activity of the enzyme. These results suggest that both CBM48 and domain C play a role in binding substrates. The crystal forms described contribute to the understanding of pullulanase domain–carbohydrate interactions.

The biological processes related to protein homeostasis in Mycobacterium tuberculosis, the etiologic agent of tuberculosis, have recently been established as critical pathways for therapeutic intervention. Proteins of particular interest are ClpC1 and the ClpC1–ClpP1–ClpP2 proteasome complex. The structure of the potent antituberculosis macrocyclic depsipeptide ecumicin complexed with the N-terminal domain of ClpC1 (ClpC1-NTD) is presented here. Crystals of the ClpC1-NTD–ecumicin complex were monoclinic (unit-cell parameters a = 80.0, b = 130.0, c = 112.0 Å, β = 90.07°; space group P21; 12 complexes per asymmetric unit) and diffracted to 2.5 Å resolution. The structure was solved by molecular replacement using the self-rotation function to resolve space-group ambiguities. The new structure of the ecumicin complex showed a unique 1:2 (target:ligand) stoichiometry exploiting the intramolecular dyad in the α-helical fold of the target N-terminal domain. The structure of the ecumicin complex unveiled extensive interactions in the uniquely extended N-terminus, a critical binding site for the known cyclopeptide complexes. This structure, in comparison with the previously reported rufomycin I complex, revealed unique features that could be relevant for understanding the mechanism of action of these potential antituberculosis drug leads. Comparison of the ecumicin complex and the ClpC1-NTD-L92S/L96P double-mutant structure with the available structures of rufomycin I and cyclomarin A complexes revealed a range of conformational changes available to this small N-terminal helical domain and the minor helical alterations involved in the antibiotic-resistance mechanism. The different modes of binding and structural alterations could be related to distinct modes of action.

Aldo-keto reductases (AKRs) are NADPH/NADP+-dependent oxidoreductase enzymes that metabolize an aldehyde/ketone to the corresponding alcohol. AKR4C14 from rice exhibits a much higher efficiency in metabolizing malondialdehyde (MDA) than do the Arabidopsis enzymes AKR4C8 and AKR4C9, despite sharing greater than 60% amino-acid sequence identity. This study confirms the role of rice AKR4C14 in the detoxification of methylglyoxal and MDA, and demonstrates that the endogenous contents of both aldehydes in transgenic Arabidopsis ectopically expressing AKR4C14 are significantly lower than their levels in the wild type. The apo structure of indica rice AKR4C14 was also determined in the absence of the cofactor, revealing the stabilized open conformation. This is the first crystal structure in AKR subfamily 4C from rice to be observed in the apo form (without bound NADP+). The refined AKR4C14 structure reveals a stabilized open conformation of loop B, suggesting the initial phase prior to cofactor binding. Based on the X-ray crystal structure, the substrate- and cofactor-binding pockets of AKR4C14 are formed by loops A, B, C and β1α1. Moreover, the residues Ser211 and Asn220 on loop B are proposed as the hinge residues that are responsible for conformational alteration while the cofactor binds. The open conformation of loop B is proposed to involve Phe216 pointing out from the cofactor-binding site and the opening of the safety belt. Structural comparison with other AKRs in subfamily 4C emphasizes the role of the substrate-channel wall, consisting of Trp24, Trp115, Tyr206, Phe216, Leu291 and Phe295, in substrate discrimination. In particular, Leu291 could contribute greatly to substrate selectivity, explaining the preference of AKR4C14 for its straight-chain aldehyde substrate.

The outer membrane of Gram-negative bacteria is highly impermeable to hydrophilic molecules of larger than 600 Da, protecting these bacteria from toxins present in the environment. In order to transport nutrients across this impermeable membrane, Gram-negative bacteria utilize a diverse family of outer-membrane proteins called TonB-dependent transporters. The majority of the members of this family transport iron-containing substrates. However, it is becoming increasingly clear that TonB-dependent transporters target chemically diverse substrates. In this work, the structure and phylogenetic distribution of the TonB-dependent transporter YncD are investigated. It is shown that while YncD is present in some enteropathogens, including Escherichia coli and Salmonella spp., it is also widespread in Gammaproteobacteria and Betaproteobacteria of environmental origin. The structure of YncD was determined, showing that despite a distant evolutionary relationship, it shares structural features with the ferric citrate transporter FecA, including a compact positively charged substrate-binding site. Despite these shared features, it is shown that YncD does not contribute to the growth of E. coli in pure culture under iron-limiting conditions or with ferric citrate as an iron source. Previous studies of transcriptional regulation in E. coli show that YncD is not induced under iron-limiting conditions and is unresponsive to the ferric uptake regulator (Fur). These observations, combined with the data presented here, suggest that YncD is not responsible for the transport of an iron-containing substrate.

l-Hydroxyproline (l-Hyp) is a nonstandard amino acid that is present in certain proteins, in some antibiotics and in the cell-wall components of plants. l-Hyp is the product of the post-translational modification of protein prolines by prolyl hydroxylase enzymes, and the isomers trans-3-hydroxy-l-proline (T3LHyp) and trans-4-hydroxy-l-proline (T4LHyp) are major components of mammalian collagen. T4LHyp follows two distinct degradation pathways in bacteria and mammals, while T3LHyp is metabolized by a two-step metabolic pathway that is conserved in bacteria and mammals, which involves a T3LHyp dehydratase and a Δ1-pyrroline-2-carboxylate (Pyr2C) reductase. In order to shed light on the structure and catalysis of the enzyme involved in the second step of the T3LHyp degradation pathway, the crystal structure of Pyr2C reductase from the archaeon Thermococcus litoralis DSM 5473 complexed with NADH and l-proline is presented. The model allows the mapping of the residues involved in cofactor and product binding and represents a valid model for rationalizing the catalysis of Pyr2C reductases.

The crystal structure of MgCoGa2 (magnesium cobalt digallide) was solved by direct methods and refined in two space groups as P21/c (standard choice) and P21/n (non-standard choice). The refined lattice parameters for the standard choice are a = 5.1505 (2), b = 7.2571 (2), c = 8.0264 (3) Å and β = 125.571 (3)°, and for the non-standard choice are a = 5.1505 (2), b = 7.2571 (2), c = 6.5464 (2) Å and β = 94.217 (3)°. All parameters for MgCoGa2 refined to R1 = 0.027 and wR2 = 0.042 using 594 reflections. The crystal structure peculiarities of this compound are discussed. Particular attention has been given to relationships with other similar structures, such as YPd2Si and Fe3C. Crystallographic analysis, together with linear muffin-tin orbital electronic structure calculations, reveals the presence of three-dimensional polyatomic nets with partial covalent bonding between the Ga atoms.