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: Serial crystallography enables extraction/purification of single-phase subsets from a mixture of multiphase diffraction snapshots.
Synopsis: This systematic study about the location, absence, networking and interactions of the conserved water molecules present in hTTR may put some light on the understanding of different structural and functional aspects of the protein. Apart from this, the present study provides some rational clues about the water mediated architecture and stability of the protein molecule.
Synopsis: The first structure of a superoxide reductase from a eukaryotic organism, Giardia intestinalis, is described at 2.0 Å resolution. The data suggest lack of redox-linked structural changes upon iron center reduction, high flexibility in the N-terminal loop of the protein and high sensitivity of the crystallized protein to radiation damage.
Synopsis: Three crystal structures of the Acetabularia rhodopsin I (ARI) protein from Acetabularia acetabulum at three different pH values have been determined, at 1.57, 1.52 and 1.80 Å resolutions. We discuss the mechanism of the photocycle of ARI, which is slower than that of Bacteriorhodopsin (BR), based on these structures and their photochemical properties.
Synopsis: X-ray free-electron laser (XFEL) crystallography is making it possible to obtain information about complex biological systems like photosystem II that cannot be obtained by other means. However, the processing of XFEL data remains a major technical challenge.
Synopsis: We present the crystal structure of a conserved domain from Burkholderia pseudomallei antigen BPSL2063 as a structural vaccinology target and report the generation of an ORF filtered library, based on a single gene and on a genomic DNA scale, as a tool for the identification of folded protein fragments, to support their production in soluble form for downstream structural/biochemical studies.
Synopsis: Hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the amount of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side chain conformation was determined.
Synopsis: Structural and enzymological binding and stability studies of wild type and mutated variants of yeast 3, 2-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.
Synopsis: Over 100 PDB depositions presented in space group P1, but in reality possessing higher symmetry, were analyzed in order to evaluate the accuracy of the unit-cell parameters of macromolecular crystals.
Synopsis: Nicotinamide mononucleotide adenylyltransferase (NMNAT) catalyzes the biosynthesis of NAD+ and NaAD+. Surprisingly, when expressed in Escherichia coli, NMNAT mutants trapped a molecule of NADP+ in their active sites. This NADP+ was bound in a conformation quite different from the one displayed by NAD+ in the native enzyme complex.
Synopsis: DosC is an oxygen-dependent diguanylate cyclase that synthesizes the bacterial second messenger cyclic di-GMP. We describe a model of the dimeric holoprotein based on assembly of high resolution structures of the sensing globin domain, the linking middle domain and the catalytic cyclase domain and present a hypothesis for its regulation.
Synopsis: 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 is developed to aid in structural refinement in macromolecular X-ray crystallography.
Synopsis: The crystal structure of glyoxalase I from Z. mays is reported.
Synopsis: A highly X-ray-transparent, silicon nitride-based device has been designed and fabricated to harvest protein microcrystals for high-resolution X-ray diffraction data collection using microfocus and XFEL beamlines.
Synopsis: A combination of crystal-contact engineering and surface-entropy reduction was used to enable the crystallization and subsequent structural solution of two spliceosomal assembly intermediates.
Synopsis: Structural and functional studies of a metallo--lactamase reveal a new type of structurally encoded nickel-containing heterodinuclear site.
Synopsis: In vitro neuromuscular studies were performed to demonstrate that suramin neutralizes the toxic activity of a PLA2-like protein, corroborating calorimetric assays. Crystallographic studies demonstrated that the inhibitor binds to the surface of the toxin, obstructing its membrane docking and disruption sites and confirming the proposed myotoxic mechanism.
Synopsis: The high-resolution structure of uracil-DNA N-glycosylase (UNG) from D. radiodurans in complex with DNA provides support for a model in which DNA compression and minor-groove stabilization is crucial for the uracil damage-detection mechanism of UNGs.
Synopsis: A method is reported for collecting room-temperature data from protein crystals under vacuum by protecting them with a thin graphene layer.
Synopsis: The self-complementary DNA decamer d(GCATGCATGC) crystallizes as an unusual double-folded structure, which serves as the basis for a possible structural model of triplet-repeat DNA sequences.
Synopsis: The crystal structure of the broadly neutralizing antibodies 8ANC195 and PGT128 bound to an HIV-1 envelope trimer has been determined. Structural and binding analyses have elucidated the full epitopes for these antibodies in the context of the intact viral glycoprotein, providing improved templates for HIV-1 vaccine design.
Synopsis: Epsilon-class glutathione S-transferases (GSTs) are found in invertebrates, including many insects, where they play roles in the detoxication of insecticides and in development. The crystal structures of two epsilon-class GSTs from D. melanogaster are reported and compared to aid in the characterization of the functional differences between the isozymes.
Synopsis: The crystal structures of two constructs of RC1339/APRc from R. conorii, consisting of either residues 105-231 or 110-231 followed by a His tag, have been determined in three different crystal forms. The monomer of APRc assumes a retropepsin-like fold, but the dimer observed in all crystal forms is entirely different from the canonical dimer of retropepsins.
Synopsis: Structural insight is provided into the mechanism by which a widespread family of bacterial chemotaxis receptors containing the periplasmic tandem Per-Arnt-Sim (PAS) sensing domain recognize free amino acids, and a model for signal transduction across the membrane is proposed.
Synopsis: The crystal structure of an Rsd-HPr complex was determined in order to reveal the binding interface between Rsd and HPr. A molecular link between global gene regulation and nutrient availability is described.
Synopsis: A new Rice function approximation for the effect of intensity measurement errors improves the treatment of weak intensity data in calculating log-likelihood gain scores in crystallographic applications including experimental phasing, molecular replacement and refinement.
Synopsis: Data collection with a tailored 50 µm diameter X-ray beam at 4.6 keV ( = 2.69 Å) at the newly established EMBL beamline P13 at PETRA III allowed the crystal structure determination of the Cdc23Nterm homodimer (65.4 kDa, 12 Cys and ten Met residues) by sulfur SAD phasing at 3.1 Å resolution while overcoming crystal twinning.
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