forthcoming articles in Acta Crystallographica Section D

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.


Accepted 27 August 2015

Serial crystallography analysis of protein isomorphous replacement data from a mixture of native and derivative(s) micro-crystals

T. Zhang, D. Yao, J. Wang, Y. Gu and H. Fan

Synopsis: Serial crystallography enables extraction/purification of single-phase subsets from a mixture of multiphase diffraction snapshots.


Accepted 26 August 2015

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

A. Banerjee, S. Dasgupta, B. P. Mukhopadhyay and K. Sekar

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.


Accepted 24 August 2015

Superoxide reductase from Giardia intestinalis: structural characterization of the first SOR from a eukaryotic organism shows an iron centre highly sensitive to photo-reduction

C. M. Sousa, P. Carpentier, P. M. Matias, F. Testa, F. Pinho, P. Sarti, A. Guiffrè, T. M. Bandeiras and C. V. Romão

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.


Accepted 21 August 2015

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

M. Furuse, J. Tamogami, T. Hosaka, T. Kikukawa, N. Shinya, M. Hato, N. Ohsawa, S. Y. Kim, K.-H. Jung, M. Demura, S. Miyauchi, N. Kamo, K. Shimono, T. Kimura-Someya, S. Yokoyama and M. Shirouzu

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.


Accepted 21 August 2015

On the statistical properties of X-ray free-electron laser crystallographic data sets

J. Wang, P. B. Moore, V. S. Batista and G. Brudvig

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.


Accepted 21 August 2015

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

L. J. Gourlay, C. Peano, C. Deantonio, L. Perletti, A. Pietrelli, R. Villa, E. Matterazzo, P. Lassaux, C. Santoro, S. Puccio, D. Sblattero and M. Bolognesi

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.


Accepted 20 August 2015

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

L. Biedermannová and B. Schneider

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.


Accepted 19 August 2015

Structures of yeast peroxisomal [Delta]3,[Delta]2- 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

G. U. Onwukwe, M. K. Koski, P. Pihko, W. Schmitz and R. K. Wierenga

Synopsis: Structural and enzymological binding and stability studies of wild type and mutated variants of yeast [Delta]3, [Delta]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.


Accepted 19 August 2015

On the accuracy of cell dimensions in protein crystallography

Z. Dauter and A. Wlodawer

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.


Accepted 18 August 2015

Nicotinamide mononucleotide adenylyltransferase displays alternate binding modes for nicotinamide nucleotides

R. Pfoh, E. F. Pai and V. Saridakis

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.


Accepted 18 August 2015

Structural analysis of an oxygen-regulated diguanylate cyclase

M. Tarnawski, T. R. M. Barends and I. Schlichting

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.


Accepted 16 August 2015

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

C. Zhang, Q. Wang and J. Ma

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.


Accepted 14 August 2015

Structure of the novel monomeric glyoxalase I from Zea mays

G. L. Turra, R. B. Agostini, C. M. Fauguel, D. A. Presello, C. S. Andreo, J. M. González and V. A. Campos-Bermudez

Synopsis: The crystal structure of glyoxalase I from Z. mays is reported.


Accepted 11 August 2015

A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

T. D. Murray, A. Y. Lyubimov, C. M. Ogata, H. Vo, M. Uervirojnangkoorn, A. T. Brunger and J. M. Berger

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.


Accepted 7 August 2015

Crystallizing the 6S and 8S spliceosomal assembly intermediates: a complex project

J.-P. Pelz, H. Schindelin, K. van Pee, J. Kuper, C. Kisker, K. Diederichs, U. Fischer and C. Grimm

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.


Accepted 6 August 2015

Structural and functional studies of a metallo-[beta]-lactamase unveil a new type of structurally encoded nickel-containing heterodinuclear site

H. Choi, H. J. Kim, A. Matsuura, B. Mikami, H.-J. Yoon and H. H. Lee

Synopsis: Structural and functional studies of a metallo-[beta]-lactamase reveal a new type of structurally encoded nickel-containing heterodinuclear site.


Accepted 6 August 2015

A history of experimental phasing in macromolecular crystallography

N. Isaacs


Accepted 31 July 2015

Structural and functional evidence for membrane docking and disruption sites on phospholipase A2-like proteins revealed by complexation with the inhibitor suramin

G. H. M. Salvador, T. R. Dreyer, W. L. G. Cavalcante, F. F. Matioli, J. I. dos Santos, A. Velazquez-Campoy, M. Gallacci and M. R. M. Fontes

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.


Accepted 27 July 2015

Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA

H. L. Pedersen, K. A. Johnson, C. E. McVey, I. Leiros and E. Moe

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.


Accepted 27 July 2015

In vacuo X-ray data collection from graphene-wrapped protein crystals

A. J. Warren, A. D. Crawshaw, J. Trincao, P. Aller, S. Alcock, I. Nistea, P. S. Salgado and G. Evans

Synopsis: A method is reported for collecting room-temperature data from protein crystals under vacuum by protecting them with a thin graphene layer.


Accepted 22 July 2015

The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences

A. Thirugnanasambandam, S. Karthik, P. K. Mandal and N. Gautham

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.


Accepted 22 July 2015

Complete epitopes for vaccine design derived from a crystal structure of the broadly neutralizing antibodies PGT128 and 8ANC195 in complex with an HIV-1 Env trimer

L. Kong, A. Torrents de la Peña, M. C. Deller, F. Garces, K. Sliepen, Y. Hua, R. L. Stanfield, R. W. Sanders and I. A. Wilson

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.


Accepted 22 July 2015

Comparison of epsilon- and delta-class gluta­thione S-transferases: the crystal structures of the gluta­thione S-transferases DmGSTE6 and DmGSTE7 from Drosophila melanogaster

M. Scian, I. Le Trong, A. M. A. Mazari, B. Mannervik, W. M. Atkins and R. E. Stenkamp

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.


Accepted 22 July 2015

Structure of RC1339/APRc from Rickettsia conorii, a retropepsin-like aspartic protease

M. Li, A. Gustchina, R. Cruz, M. Simões, P. Curto, J. Martinez, C. Faro, I. Simões and A. Wlodawer

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.


Accepted 21 July 2015

Structural basis for amino-acid recognition and transmembrane signalling by tandem Per-Arnt-Sim (tandem PAS) chemoreceptor sensory domains

Y. C. Liu, M. P. Machuca, S. A. Beckham, M. J. Gunzburg and A. Roujeinikova

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.


Accepted 20 July 2015

Structural basis for the sequestration of the anti-[sigma]70 factor Rsd from [sigma]70 by the histidine-containing phosphocarrier protein HPr

Y.-H. Park, S.-H. Um, S. Song, Y.-J. Seok and N.-C. Ha

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.


Accepted 9 July 2015

A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error

R. J. Read and A. J. McCoy

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.


Accepted 27 May 2015

Data collection with a tailored X-ray beam size at 2.69 Å wavelength (4.6 keV): sulfur SAD phasing of Cdc23Nterm

M. Cianci, M. R. Groves, D. Barford and T. R. Schneider

Synopsis: Data collection with a tailored 50 µm diameter X-ray beam at 4.6 keV ([lambda] = 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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