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: Three-dimensional structure of green fluorescent protein NowGFP (succesor of Cerulean) with an anionic tryptophan-based chromophore and that of NowGFP_conv in the photoconverted form. Relation between structure and photophysical characteristics
Synopsis: The LpfD protein represents the tip adhesin of enterobacteriaceal Long Polar Fimbriae and LpfD of the adherent invasive E. coli strain LF82 directs LPF binding towards the intestinal epithelium and underlying tissue.
Synopsis: Deerpoxvirus employs the cell death inhibitor DPV022 to prevent premature host cell death by engaging pro-death Bcl-2 proteins via two independent ligand binding sites as part of a domain-swapped Bcl-2 fold.
Synopsis: The crystal structures of the solubilized domain of cytochrome b5 from porcine liver were determined at sub-Â resolutions in two crystal forms for both the oxidized and reduced states. The high-resolution structures provided information about factors important for regulating the electronic properties of the heme group of cytochrome b5.
Synopsis: The crystal structure of the phosphatidylinositol 4-kinase (PI4K) II reveals new details such as the high conformational heterogeneity of the lateral hydrophobic pocket, and, together with the structure of PI4K II with a nucleoside analogue, provides structural basis for isoform-specific inhibitor design.
Synopsis: Three crystal structures of L-galactitol-1-phosphate 5-dehydrogenase from Escherichia coli have been solved. The functional data were combined with the structural results to understand the enantioselectivity of this enzyme.
Synopsis: The crystal structure of the phosphatase domain of MTMR8 provides insights into its dimerization, membrane association, and reversible regulation.
Synopsis: Seventeen independent crystal structures of family I uracil-DNA glycosylase from M. tuberculosis (MtUng) and their complexes with uracil and its derivatives, distributed among five distinct crystal forms, provide information on conformational selection on DNA binding, segmental mobility and protein-ligand interactions.
Synopsis: The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a Thermatoga maritima enzyme has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template.
Synopsis: The structure of Clostridium perfringens Sortase D was determined at 1.99 Å resolution. Comparative biochemical and structural analyses revealed that this transpeptidase may represent a new subclass of the Sortase D family.
Synopsis: Controlled dehydration of IE1 crystals leads to molecular rearrangements that trigger a space-group transition from P21 to P43 with a concomitant reduction of the number of IE1 chains in the asymmetric unit. Analysis of the pre- and post-dehydration structures reveals a reshaping of the tertiary structure of IE, which possibly informs on the mechanism by which IE1 binds to host-cell target proteins.
Synopsis: The X-ray structure of protease-cleaved Escherichia coli -2-macroglobulin is described, which reveals a putative mechanism of activation and conformational change essential for protease inhibition.
Synopsis: A method is presented to detect peptide bonds that need either a trans-cis flip or a peptide-plane flip.
Synopsis: The intercalation of SHG active dyes into formed protein crystals has allowed the enhancement of second-harmonic generation signal from protein crystals by 1000-fold.
Synopsis: The correlation of histidine-ring geometry with the protonation state was analyzed in structures in the PDB and CSD. 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 T. cruzi histidyl-tRNA synthetase.
Synopsis: The structure of the histidine kinase associated with the light-oxygen-voltage domain from B. 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 from 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: 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: The crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment is reported at a resolution of 2 Å. A new mode of DNA recognition for HMG box proteins is found in which two box A domains bind in an unusual configuration generating a highly kinked DNA structure.
Synopsis: A generalization of the ScrewFit method for protein secondary-structure description and analysis is presented which uses only the positions of the C atoms and describes the winding of the protein main chain as a succession of screw motions which link consecutive residue-based Frenet frames on the discrete C space curve.
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.
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