Deformable complex network for refining low-resolution X-ray structures

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.

Structural analysis of an oxygen-regulated diguanylate cyclase

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.

Structures of yeast peroxisomal Δ³,Δ²-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the catalytic base and the oxyanion hole

Structural and enzymological binding and stability studies of wild-type and mutated variants of yeast Δ³,Δ²-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.

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

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.

Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum

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.

On the accuracy of unit-cell parameters in protein crystallography

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.

Selecting soluble/foldable protein domains through single-gene or genomic ORF filtering: structure of the head domain of Burkholderia pseudomallei antigen BPSL2063

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.

Superoxide reductase from Giardia intestinalis: structural characterization of the first SOR from a eukaryotic organism shows an iron centre that is highly sensitive to photoreduction

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.

The putative role of some conserved water molecules in the structure and function of human transthyretin

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.

Structure of AadA from Salmonella enterica: a monomeric aminoglycoside (3′′)(9) adenyltransferase

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.

The structure of the GemC1 coiled coil and its interaction with the Geminin family of coiled-coil proteins

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.

Crystallographic study of a MATE transporter presents a difficult case in structure determination with low-resolution, anisotropic data and crystal twinning

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.

Structure and inhibition of subunit I of the anthranilate synthase complex of Mycobacterium tuberculosis and expression of the active complex

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.

Structural insight and flexible features of NS5 proteins from all four serotypes of Dengue virus in solution

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.

MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines

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.

The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer–Villiger monooxygenase

The first crystal structure of a type II Baeyer–Villiger monooxygenase reveals a different ring orientation of its FMN cofactor compared with other related bacterial luciferase-family enzymes.

Structural insights into the interaction of human IgG1 with FcγRI: no direct role of glycans in binding

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.

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