Subscribe: Forthcoming article in Acta Crystallographica Section D: Biological Crystallography
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Forthcoming article in Acta Crystallographica Section D Structural Biology



Acta Crystallographica Section D: Structural Biology welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports o



 



A public database of macromolecular diffraction experiments
The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) is a large, scalable and searchable web-accessible archive of protein crystallography diffraction experiments organized according to metadata.



Automated refinement of macromolecular structures at low resolution using prior information
An automated pipeline for low-resolution structure refinement (LORESTR) has been developed to assist in the hassle-free refinement of difficult cases. The pipeline automates the selection of high-resolution homologues for external restraint generation and optimizes the parameters for ProSMART and REFMAC5, improving R factors and geometry statistics in 94% of the test cases.



Using more than 801,296 small molecule crystal structures to aid in protein structure refinement and analysis
A guide to how the Cambridge Structural Database can be used to aid macromolecular crystallography.



Conservation in the mechanism of glucuronoxylan hydrolysis revealed by the structure of glucuronoxylan xylanohydrolase (CtXyn30A) from Clostridium thermocellum
The thermostable glucuronoxylan endo-β-1,4-xylanase from C. thermocellum cleaves the xylan chain specifically at sites containing 4-O-methylglucuronic acid substitutions. The structure of the ligand-bound enzyme mutant E225A solved at 1.17 Å resolution shows binding of the xylotetraose-cleavage oligosaccharides at subsites −3 to +2.



PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps
A new approach is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from three-dimensional electron microscopy.



Glycoblocks: a schematic three-dimensional representation for glycans and their interactions
With structural glycoscience finally gaining popularity, the need for a clear way of depicting glycans and their interactions in three dimensions is more pressing than ever. Here the Glycoblocks representation is introduced, which combines a simplified bonding-network depiction with the familiar two-dimensional glycan notation brought into three-dimensions.



Manipulation of an existing crystal form unexpectedly results in interwoven packing networks with pseudo-translational symmetry
A nonribosomal peptide synthetase di-domain construct was produced using known crystal packing as a guide, and the resulting crystal has an unanticipated packing.



Empirical power laws for the radii of gyration of protein oligomers
Power laws describing the dependence of the radius of gyration on the number of residues are calculated for protein oligomers. The power laws are useful for predicting the oligomeric state from small-angle X-ray scattering, identifying elongated proteins and validating the annotation of biological assemblies.



Validation and correction of Zn–CysxHisy complexes
A method is presented to automatically validate and correct Zn–CysxHisy complexes that have a distorted tetrahedral geometry.



Crystal structures of the disulfide reductase DsbM from Pseudomonas aeruginosa
High-resolution structures of the cytosolic disulfide reductase DsbM in apo and S-glutathionylated states are described.



Online ion-exchange chromatography for small-angle X-ray scattering
SAXS coupled with online ion-exchange chromatography allows the collection of high-quality BioSAXS data.



Determination of crystal structures of proteins of unknown identity using a marathon molecular replacement procedure: structure of Stenotrophomonas maltophilia phosphate-binding protein
The structure of a serendipitously crystallized protein was determined using a large-scale molecular replacement protocol, and on the basis of the sequence deduced from the electron-density map the protein was identified as a phosphate-binding protein from S. maltophilia.



WONKA and OOMMPPAA: analysis of protein–ligand interaction data to direct structure-based drug design
The background to and development of WONKA and OOMMPPAA, tools for structure-based drug design, is described.