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: We estimate current and attainable coverage by the X-ray structures of proteins and their functions on scale of the "protein universe". We performed detailed analysis of coverage across nearly 2,000 proteomes in all superkingdoms of life and functional annotations, and with particular focus on human proteome and the family of GPCR proteins.
Synopsis: Four enzyme-substrate complex structures of CYP154C5 from Nocardia farcinica with steroids pregnenolone, progesterone, androstenedione and testosterone bound in the enzyme's active site are reported revealing structural determinants for CYP154C5's high regio- and stereoselectivity in steroid hydroxylation.
Synopsis: The structure of discoidin domain from mouse muskelin is determined and an analysis on the inter-domain interaction suggests the mechanism for self-association.
Synopsis: H. pylori Csd4 (HP1075), together with other peptidoglycan hydrolases, plays an important role in determining the helical cell shape. Its crystal structure has been determined in three different forms.
Synopsis: The three-dimensional structure of the GH27 arabinopyranosidase (Abp) from Geobacillus stearothermophilus T6 has been determined by molecular replacement, leading to full structural analysis of Abp-WT (at 2.28 Å resolution) and its catalytic mutant Abp-D197A with (2.20 Å) and without (2.30 Å) a bound L-arabinose product. The structures demonstrate that Abp is a tetramer built of two pincer-like dimers, as also confirmed by SAXS.
Synopsis: The present work illustrates that small angle neutron scattering, deuteration and contrast variation, combined with in vitro particle reconstruction, constitutes a very efficient approach to determine subunit architectures in large, symmetric protein complexes. In the case of the 468-kDa hetero-dodecameric TET peptidase machine, it allowed us to demonstrate that the assembling of the 12 subunits is a highly controlled process and represents a way to optimize the enzyme's catalytic efficiency.
Synopsis: The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) is a new initiative for the structural biology community, following the success of CCP4 for macromolecular crystallography. We report progress in supporting users and developers of cryoEM software.
Synopsis: The rate of global radiation damage to 70S ribosome crystals has been measured at 100 K, 180 K, and 300 K. At 100 K and 300 K, damage rates are comparable to and much larger than those of model proteins, respectively. Larger damage rates at 300 K cannot explain the dramatically higher diffraction quality observed at 100 K.
Synopsis: The Campylobacter jejuni phosphoethanolamine transferase EptC functions in antibacterial resistance, motility, and host intestinal colonization. In this study, we report the three-dimensional structure of the catalytic domain of EptC in a covalent phospho-enzyme intermediate state. EptC active-site mutant strains of C. jejuni demonstrate the potential for EptC enzyme inhibitors.
Synopsis: The X-ray structure of the N-terminal acetyltransferase domain (AAC(6')-Ie) of the bifunctional antibiotic resistance enzyme, AAC(6')-Ie-APH(2")-Ia, has been determined as a ternary kanamycin/coenzyme-A complex. X-ray structures of the isolated AAC(6')-Ie and APH(2")-Ia domains, combined with small-angle X-ray scattering (SAXS) data, allow for the determination of the structural architecture of the full-length bifunctional enzyme in solution.
Synopsis: A robust and transferable algorithm is presented to objectively describe and rank robotically captured images of crystallization droplets according to their likelihood of crystalline behaviour for efficient and accurate identification of successful crystallization.
Synopsis: High-multiplicity data were used to solve the West Nile virus NS1 structure by S-SAD and for the extension of useable resolution for refinement.
Synopsis: A case study on the treatment of SIRAS data using the originally unknown protein LegC3N is described. An iterative direct-method-based treatment was proposed that led to improved results in this particular test case.
Synopsis: The crystal structure of arabinose-5-phosphate isomerase from B. fragilis NCTC 9343 in complex with an endogenous ligand, CMP-Kdo, is described. Structural and sequence comparisons suggest highly conserved functional residues in the active site that could be targeted for antibacterial drug design.
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: A new indexing method is presented which is capable of indexing multiple crystal lattices from narrow wedges of data. The efficacy of this method is demonstrated with both semi-synthetic multi-lattice data and real multi-lattice data recorded from microcrystals of 1 µm in size.
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.
Synopsis: The thermostability of the -carbonic anhydrase from the thermophilic bacterium T. ammonificans is shown to depend on the 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 owing to its increased structural rigidity.
Synopsis: Rank scaling of Fourier syntheses leads to new tools for the comparison of 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 global conformations and sequence homology of the compared macromolecules. This allows quick and intuitive visualization of the conservation of backbone and side-chain conformations, providing complementary information 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 in hydroxymethylome mapping based on the crystal structure of PvuRts1I.
Synopsis: Cthe_2159 is a member of a domain of unknown function) family (DUF4353 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 for solution of the 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 that differs from that of other SarA homologues.
Synopsis: 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: The first X-ray structure of a 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP at a resolution of 2.2 Å is reported. This structure establishes that the enzyme adopts the cupin-fold, forming compact dimers with a pronounced hydrophobic interface between the monomers. Each monomer possesses a catalytic ferrous iron that is coordinated by three histidines (76, 78 and 114) and an additional ligand which has been putatively assigned as a carbonate, although formate and acetate are possibilities.
Synopsis: Pseudo-symmetry, which is common in macromolecular crystals, may result in incorrect space-group assignment that remains unnoticed until the advanced stages of refinement. The program Zanuda has been developed to automate space-group assignment and validation.
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: 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: 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: 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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