The 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: The correlation of histidine ring geometry with the protonation state was analyzed in PDB and CSD structures. In conclusion, revised stereochemical restraints for histidine are proposed.
Synopsis: A crystallographic cocktail screening campaign against 680 fragments revealed a binding hotspot in the structure of Trypanosoma cruzi histidyl-tRNA synthetase.
Synopsis: The structure of the histidine kinase associated with the light-oxygen-voltage domain from Brucella abortus, containing 968 amino acids in the asymmetric unit, was solved using the "off edge" anomalous signal from sulfur to a resolution of 2.90 Å by combining data from several isomorphous crystals (space group P21) as well as data collected in multiple orientations of the same crystal (true redundancy), stressing the importance of the latter approach in off edge S-SAD. A second construct that has a shorter cloning artifact enabled the production of improved crystals and subsequent refinement of the structure to 2.51 Å resolution.
Synopsis: Full-length structure of the major autolysin LytA from Streptococcus pneumoniae combined with the enzymatic activity assays suggest that dimerization and full occupancy of all choline-binding sites are indispensable for the full activity of LytA in vivo.
Synopsis: A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different Translation-Libration-Screw refinement strategies produce unique diffuse intensity patterns.
Synopsis: We report the crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment at a resolution of 2 Å. We find a new mode of DNA recognition for HMG box proteins, where two box A domains bind in an unusual configuration generating a highly kinked DNA structure.
Synopsis: The complex structures of HaG and its mutants revealed the substrate specificity and catalytic mechanism of HaG.
Synopsis: The PPM II phosphatase RsbX features a catalytic centre that binds two Mn2+ ions with five residues instead of the usual four as in PPM I phosphatases, with a conformational reorganization that tilts a flexible loop towards the second Mn2+ ion for the fifth residue to coordinate it.
Synopsis: datasw, a novel tool for rapid processing of HPLC-SAXS data.
Synopsis: We present an updated partiality model and post-refinement algorithm for XFEL snapshot diffraction data, confirmed by observing anomalous density for sulfur atoms at an X-ray wavelength of 1.3 Å.
Synopsis: Crystal structures of the GH130 enzyme Uhgb_MP in the apo form and in complex with mannose and N-acetylglucosamine are described and the structural determinants of the functional specificities of enzymes involved in N-glycan breakdown by human gut bacteria are identified.
Synopsis: AcdDPN7 is a novel desulfinase, which catalyzes the sulfur abstraction in the catabolic pathway of 3,3'-dithiodipropionic acid (DTDP). The crystal structures of the native AcdDPN7 at 1.89 Å resolution and the native AcdDPN7 soaked with the substrate analog succinyl-CoA at 2.30 Å resolution revealed an acyl-CoA dehydrogenase fold with Arg84 as a key residue in the desulfination reaction.
Synopsis: Models of crystal structures deposited in the Protein Data Bank for protein complexes of cisplatin and carboplatin appear to have troubling crystallographic problems and to exhibit significant departures from the known principles of chemistry. They may serve as examples of what should be improved in the deposition and presentation of macromolecular models and how to handle deposition of the results of re-refinement of crystallographic data.
Synopsis: The crystal structure of the homology domain of the subunit of the bovine COPI complex was determined to 2.15 Å resolution. The structure reveals important aspects of interdomain flexibility that relate to the function of COPI.
Synopsis: On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity.
Synopsis: The hexameric structure of truncated A. aeolicus FtsH shows a molecular architecture that forms two rings, in which the ATPase ring possesses twofold symmetry and the protease ring possesses sixfold symmetry. The importance of a dynamic -strand in the active site and a conserved glycine in the linker region is demonstrated in the full-length protein by site-directed mutagenesis.
Synopsis: The crystal structure of fission yeast Dis3l2 displays an open conformation that differs from that in the mouse Dis3l2-RNA complex.
Synopsis: S. aureus steals iron in the form of haem from human haemoglobin (Hb). The crystal structure of the S. aureus Hb receptor IsdH in complex with Hb shows that the receptor induces a conformational change in the globin haem pocket that may promote haem transfer.
Synopsis: Statistical surveys of the protein structure database combined with quantum-mechanical calculations reveal a systematic dependence of bond distances on conformation. Interestingly, the variability of backbone C-O and C-N distances is not directly related to peptide-bond planarity.
Synopsis: The structure of the giant haemoglobin from G. paulistus was determined.
Synopsis: A method for performing high-throughput in situ serial X-ray crystallography with soluble and membrane proteins in the lipid cubic phase is described. It works with microgram quantities of protein and lipid (and ligand when present) and is compatible with the most demanding sulfur SAD phasing.
Synopsis: The X-ray structure determination of an integral membrane protein using synchrotron diffraction data measured in situ at room temperature is demonstrated.
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