issue contents

Journal logoBIOLOGICAL
CRYSTALLOGRAPHY
ISSN: 1399-0047

November 2015 issue

Highlighted illustration

Cover illustration: MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines (Zander et al., p. 2328).

research papers


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A new refinement algorithm called the deformable complex network that combines a novel angular network-based restraint with a deformable elastic network model in the target function has been developed to aid in structural refinement in macromolecular X-ray crystallography.

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DosC is an oxygen-dependent diguanylate cyclase that synthesizes the bacterial second messenger cyclic di-GMP. A model of the dimeric holoprotein is described based on the assembly of high-resolution structures of the sensing globin domain, the linking middle domain and the catalytic cyclase domain, and a hypothesis for its regulation is presented.

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Structural and enzymological binding and stability studies of wild-type and mutated variants of yeast Δ32-enoyl-CoA isomerase, a member of the crotonase superfamily, demonstrate and rationalize the importance of helix 10 and Arg100 for the catalytic efficiency of this enzyme.

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The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined.

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Three crystal structures of the Acetabularia rhodopsin I (ARI) protein from A. acetabulum at three different pH values have been determined at 1.57, 1.52 and 1.80 Å resolution. The mechanism of the photocycle of ARI, which is slower than that of bacteriorhodopsin, is discussed based on these structures and their photochemical properties.

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A number of PDB depositions that are presented in space group P1 but in reality possess higher symmetry were analyzed in order to evaluate the accuracy of the unit-cell parameters of macromolecular crystals.

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The crystal structure of a conserved domain of B. pseudomallei antigen BPSL2063 is presented as a structural vaccinology target and the generation of an ORF-filtering library is reported, based on a single-gene and on a genomic DNA scale, as a tool for the identification of folded protein fragments in order to support their production in soluble form for downstream structural/biochemical studies.

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The first structure of a superoxide reductase from a eukaryotic organism, G. intestinalis, is described at 2.0 Å resolution. The data suggest a lack of redox-linked structural changes upon iron-centre reduction, high flexibility in the N-terminal loop of the protein and high sensitivity of the crystallized protein to radiation damage.

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This systematic study of the location, absence, networking and interactions of the conserved water molecules present in human transthyretin may shed some light on various structural and functional aspects of the protein. In addition to this, the present study provides some rational clues about the water-mediated architecture and stability of the protein molecule.

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The crystal structure of the aminoglycoside-adenylating enzyme AadA is reported together with functional experiments providing insights into its oligomeric state, ligand binding and catalysis.

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The GemC1 coiled-coil structure has subtle differences compared with its homologues Geminin and Idas. Co-expression experiments in cells and biophysical stability analysis of the Geminin-family coiled coils suggest that the GemC1 coiled coil alone is unstable.

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The structure determination of a MATE multidrug transporter is reported, which was hampered by poor data quality and crystal twinning. The lessons learned from this work may be valuable for analyzing X-ray data with similar issues.

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The anthranilate synthase (AS) complex from Mycobacterium tuberculosis has been expressed and the crystal structure of its major subunit has been solved. Inhibition studies suggest that inhibitors could be designed to inhibit both AS and other chorismate-utilizing enzymes.

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The Dengue virus NS5 proteins from all four serotypes are elongated and flexible in solution, with DENV-4 NS5 being more compact than the others. The methyltransferase domain, along with the ten-residue linker, contributes to the flexibility and is positioned at the top of the RNA-dependent RNA polymerase domain in solution.

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The fully automated collection and merging of partial data sets from a series of cryocooled crystals of biological macromolecules contained on the same support is presented, as are the results of test experiments carried out on various systems.


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In an effort to identify the critical structural features responsible for the high-affinity interaction of IgG1 Fc with FcγRI, the structure of the corresponding complex was solved at a resolution of 2.4 Å.

book reviews


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