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-carbonic anhydrase from Thermovibrio ammonificans reveals a core formed around intermolecular disulfides that contribute to its thermostabilityThe following articles are a selection of those recently accepted for publication in Acta Crystallographica Section D: Biological Crystallography.
See also Forthcoming articles in all IUCr journals.
Synopsis: Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible.
Synopsis: The biophysical characterization of protein-ligand interactions in solution by techniques such as thermal shift assay, or on surfaces using for example Dual Polarization Interferometry, plays an increasingly important role to complement crystal structure determinations.
-carbonic anhydrase from Thermovibrio ammonificans reveals a core formed around intermolecular disulfides that contribute to its thermostabilitySynopsis: The thermostability of the -carbonic anhydrase from the thermophilic bacterium Thermovibrio ammonificans is shown to depend on formation of intrasubunit disulfide bonds and a unique intersubunit disulfide/lysine core at the centre of the tetrameric molecule. Unlike most -carbonic anhydrases this enzyme does not show esterase activity towards p-nitrophenyl acetate which is proposed to be due to its increased structural rigidity.
Synopsis: An overview of applications of the deformable elastic network (DEN) refinement method is presented together with recommendations of its optimal usage.
Synopsis: Rank scaling of Fourier syntheses leads to new tools for comparison crystallographic contour maps. The new metrics are in better agreement with a visual map analysis than the conventional map correlation coefficient.
Synopsis: The Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed to allow local comparative structural analyses independent of the compared macromolecules' global conformations and sequence homology. This allows quick and intuitive visualization of the conservation of backbone and side chain conformations, providing information complementary to existing methods.
Synopsis: The crystal structure of PvuRts1I was determined and a 5-hydroxymethylcytosine binding pocket was identified in the SRA-like domain. Enzyme variants were engineered to assist hydroxymethylome mapping based on the crystal structure of PvuRts1I.
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-helix proteins with similarities to the polysaccharide lyasesSynopsis: Cthe_2159 is a member of the domain of unknown function (DUF4353) family and was identified from the C. thermocellum genome by its ability to bind cellulose. The structure was determined using Gadolinium SAD phasing and shows structural features that are highly similar to some Polysaccharide Lyase families.
Synopsis: Details of the RNA polymerase I crystal structure determination provide a framework to solve structures of other multi-subunit complexes. Simple crystallographic experiments are described to extract relevant biological information, such as the location of the enzyme active site.
Synopsis: The crystal structure of Rot shows a unique pattern of dimerization differing from that of other SarA homologues.
-lactamase homologue from a metagenomic librarySynopsis: The crystal structure of Est-Y29, a metagenomic homologue of the penicillin-binding protein/-lactamase family, was determined at 1.70 Å resolution. The biochemical properties of Est-Y29 were also investigated for potential biotechnological applications.
Synopsis: The current version of the in crystallo optical spectroscopy facility Cryobench of the ESRF is presented. The diverse experiments that can be performed at the Cryobench are also reviewed.
Synopsis: We describe why the analysis of optical absorption and Raman spectroscopic data measured from protein crystals is particularly challenging and how the SLS-APE software toolbox supports scientists in dealing with such data.
Synopsis: Pseudo-symmetry, which is common in macromolecular crystals, may result in incorrect space-group assignment that is unnoticed until advanced stages of refinement. The program Zanuda has been developed to automate space-group assignment and validation.
Synopsis: The structure of the C-terminal domain of the Zaire ebolavirus nucleoprotein (NP), encompassing residues 641-739, was determined in two distinct crystal forms. The domain has a novel fold that is distantly related to the -grasp fold.
Synopsis: Commercially available adhesives have been evaluated for crystal mounting when undertaking complex macromolecular crystallography experiments. Here, their use as tools for advanced sample mounting and cryoprotection is assessed and their suitability for room-temperature data-collection and humidity-control studies is investigated.
Synopsis: The crystal structure of full-length PRMT7 from M. musculus refined at 1.7 Å resolution is reported and provides structural clues for the monomethylation of arginine.
Synopsis: The TraN structure shows an internal dimer fold with helix-turn-helix motifs at both ends. The protein is a double-stranded DNA-binding protein that binds upstream of the pIP501 oriT, presumably acting as a type IV secretion-system regulator involved in early steps of conjugative transfer.
Synopsis: The recorded pH of protein crystallization screens is often inaccurate. Here, a method has been developed for the high-throughput measurement of pH for these screens using an acid-base indicator and a spectrophotometer.
Synopsis: A novel direct phase-selection method to select optimized phases from the ambiguous phases of a subset of reflections to replace the corresponding initial SAD phases has been developed. With the improved phases, the completeness of built residues of protein molecules is enhanced for efficient structure determination.
Synopsis: A review and discussion of the potentialities and limitations of bio-macromolecular modelling of small angle scattering data with a focus on the impact of complementary NMR restraints and a hydration shell.
Synopsis: A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein.
Synopsis: Cellobiohydrolase Cel7A from H. grisea var. thermoidea showed a 10°C higher Tm and a 75% higher yield than H. jecorina Cel7A in a performance assay at 65°C. The crystal structure at 1.8 Å resolution indicates higher flexibility in tunnel-defining loops and reveals a new loop conformation near the active centre.
Synopsis: Mushroom tyrosinase isoform abPPO4 (Agaricus bisporus polyphenol oxidase 4) was crystallized by means of an Anderson-type polyoxometalate. The enzyme crystallized as a heterodimer containing the zymogen (L-TYR; 64 kDa), the 21 kDa smaller activated form (A-TYR) and the polyoxoanion (POM) within one single crystal in a 1:1:1 ratio.
Synopsis: The crystal structure of Satellite tobacco mosaic virus (STMV) at 1.4 Å resolution represents the highest resolution and most precise native virus structure, utilizing more than twice as many reflections in refinement as were used for the previous STMV model. New details regarding the multiple ion arrangement on fivefold axes, the disposition of the `free' nucleotide, alternate conformations of amino-acid side chains and the distortion of the capsid from strict icosahedral symmetry have emerged.
Synopsis: A 2.3 Å resolution crystal structure of human EndoV was determined and the structural basis of its unusual substrate specificities was explored.
Synopsis: Anomalous diffraction signals may be routinely enhanced for native-SAD analysis by merging multi-crystal data sets at 6 keV.
Synopsis: Atomic resolution structures of cytochromes c6 and c6C from Synechococcus sp. PCC 7002 as well as their haem-pocket point mutants are presented. The biophysical and structural properties of these proteins have been characterized with particular focus on the relationship between the structure of the haem-binding pocket and the redox potential.
Synopsis: Interleukin-11 is a multifunctional member of the interleukin-6 family of cytokines. The crystal structure of human interleukin-11 is reported, providing important structural details of the receptor binding regions and revealing structural differences form the archetypal family member, interlekin-6.
Synopsis: The 2.40 Å resolution crystal structure of MSMEG_5817 revealed structural homology to sterol carrier proteins, suggesting a lipid-transport role in the survival of mycobacteria within host macrophages.
Synopsis: A set of quantitative techniques is suggested for assessing SAXS data quality. These are applied in the form of a script, SAXStats, to a test set of 27 proteins showing that these techniques are more sensitive than manual assessment of data quality.
Synopsis: Comparison of mutant and wild-type hammerhead ribozyme structures reveals active-site structural perturbations consistent with either a general base catalytic mechanism, as previously assumed to be operative in the hammerhead ribozyme, or a specific base catalytic mechanism, which may possess additional explanatory power.
Synopsis: Very little information is available in the literature concerning experimental, heavy atom phasing of membrane protein structures where the crystals have been grown using the lipid cubic phase (in meso) method. In this paper, pre-labelling, co-crystallization, soaking, site-specific mercury binding to genetically engineered single cysteine mutants, and seleno-methionine labelling as applied to an integral membrane kinase crystallized in meso are described. An assay to assess cysteine accessibility for mercury labelling of membrane proteins is introduced.
Synopsis: Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of stoichiometry, affinity, and cooperativity of multi-site interactions. We review principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT, describe their complementarity in GMMA, and present a new GMMA simulation tool set in SEDPHAT.
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