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 1 July 2015

Advances in MR procedures: the REVAN pipeline

B. Carrozzini, G. L. Cascarano, C. Giacovazzo and A. Mazzone

Synopsis: The pipeline REVAN for automatic protein crystal structure solution via molecular replacement and density guided optimization algorithms is described.

Accepted 30 June 2015

Structure of 34 kDa F-actin bundling protein ABP34 from Dictyostelium discoideum

M.-K. Kim, J.-H. Kim, J.-S. Kim and S.-O. Kang

Synopsis: The crystal structure of 34 kDa F-actin bundling protein ABP34 from Dictyostelium discoideum is reported.

Accepted 30 June 2015

An alternative RNA polymerase I structure reveals a dimer hinge

D. Kostrewa, C.-D. Kuhn, C. Engel and P. Cramer

Synopsis: The crystal structure of RNA polymerase I in an alternative crystal form at 5.5 A resolution with three dimers in a pseudo-heptagonal helical arrangement is reported. The angle between monomers in the three dimers differs markedly to that of previously reported high-resolution structures.

Accepted 24 June 2015

Structural and biophysical characterization of the [alpha]-carbonic anhydrase from the gammaproteobacterium Thiomicrospira crunogena XCL-2: insights into engineering thermostable enzymes for CO2 sequestration

N. A. Díaz-Torres, B. P. Mahon, C. D. Boone, M. A. Pinard, C. Tu, R. Ng, M. Agbandje-McKenna, D. Silverman, K. Scott and R. McKenna

Synopsis: The crystal structure of the [alpha]-carbonic anhydrase ([alpha]-CA) from Thiomicrospira crunogena XCL-2 Gammaproteobacterium has been determined to 2.6 Å resolution, and reveals features that provides it with thermal and pH stability not seen in human [alpha]-CAs.

Accepted 23 June 2015

Cap-domain closure enables diverse substrate recognition by a C2-type haloacid dehalogenase-like sugar phosphatase PfHAD1

J. Park, A. M. Guggisberg, A. R. Odom and N. H. Tolia

Synopsis: The crystal structures of PfHAD1 in complex with three different substrates were solved in order to understand how cap domain movement enables diverse substrate recognition by this sugar phosphatase.

Accepted 22 June 2015

The fully automatic characterization and data collection from crystals of biological macromolecules

O. Svensson, S. Malbet-Monaco, A. Popov, D. Nurizzo and M. W. Bowler

Synopsis: A fully automatic system has been developed that performs X-ray centring, characterization and data collection from large numbers of cryocooled crystals without human intervention.

Accepted 22 June 2015

Structure of shikimate kinase in complex with shikimate, an in vivo essential metabolic enzyme in the nosocomial pathogen Acinetobacter baumannii

K. A. Sutton, J. Breen, U. MacDonald, J. M. Beanan, R. Olson, T. Russo, L. W. Schultz and T. C. Umland

Synopsis: Shikimate kinase was determined to be essential for Acinetobacter baumannii growth and survival in a rat soft-tissue infection model. The crystal structure of this enzyme in complex with shikimate and SO42- was determined to 1.91 Å resolution, revealing the ligand-induced conformational changes of key motifs.

Accepted 22 June 2015

Insights into stabilizing interactions in the distorted domain swapped dimer of Salmonella typhimurium survival protein

Y. K. Mathiharan, H. S. Savithri and M. R. N. Murthy

Synopsis: In this manuscript, we address some interesting aspects of domain swapping, which is a unique way of protein oligomerization. Our interest in the present manuscript is to understand the role of the interfaces and hinge regions in domain swapping.

Accepted 19 June 2015

Accounting for partiality in serial crystallography using ray-tracing principles

L. M. J. Kroon-Batenburg, A. M. M. Schreurs, R. B. G. Ravelli and P. Gros

Synopsis: Serial crystallography generates partial reflections from still diffraction images. Partialities are estimated with EVAL ray tracing simulations thereby improving merged reflection data to a similar quality as conventional rotation data.

Accepted 12 June 2015

From deep TLS validation to ensembles of atomic models built from elemental motions

A. Urzhumtsev, P. V. Afonine, A. H. Van Benschoten, J. S. Fraser and P. D. Adams

Synopsis: Procedures are described for extracting the vibration and libration parameters corresponding to a given set of TLS matrices and simultaneous their validation. Knowledge of these parameters allows for the generation of structural ensembles corresponding to these matrices.

Accepted 9 June 2015

A conformational change in the peripheral anionic site of Torpedo californica acetylcholinesterase induced by a bis-imidazolium oxime

P. M. Legler, I. Soojhawon and C. B. Millard

Synopsis: Many small-molecule compounds have been shown to bind the peripheral anionic site (PAS) of acetylcholinesterase, but only a few have been shown by X-ray crystallography to induce specific structural changes in the enzyme. Here, an unexpected conformational change observed in the PAS upon the binding of an experimental bis-imidazolium oxime nerve agent antidote is reported and the observed structures are correlated with measured binding and reactivation kinetics.

Accepted 7 June 2015

The first crystal structure of a glycoside hydrolase family 17 [beta]-1,3-glucanosyltransferase displays a unique catalytic cleft

Z. Qin, Q. Yan, J. Lei, S. Yang, Z. Jiang and S. Wu

Synopsis: The crystal structures of a novel glycoside hydrolase (GH) family 17 [beta]-1,3-glucanosyltransferase from R. miehei (RmBgt17A) and two different substrate complexes have been solved at resolutions of 1.30, 2.30 and 2.27 Å, respectively. The first crystal structure of a GH family 17 [beta]-1,3-glucanosyltransferase may be useful in studies of the catalytic mechanism of GH family 17 proteins and provides a basis for further enzymatic engineering or antifungal drug screening.

Accepted 4 June 2015

ARCIMBOLDO_LITE: single-workstation implementation and use

M. Sammito, C. Millán, D. Frieske, E. Rodríguez-Freire, R. J. Borges and I. Usón

Synopsis: ARCIMBOLDO solves the phase problem through massive combination of small fragments and density modification. The use and performance of the single-workstation implementation is described.

Accepted 3 June 2015

An unexpected reactivity of the P460 cofactor in hydroxylamine oxidoreductase

A. Dietl, W. Maalcke and T. R. M. Barends

Synopsis: An unexpected reactivity is found in a unique haem moiety bound covalently to an oxidase.

Accepted 2 June 2015

Three-dimensional structure of the human breast cancer resistance protein (BCRP/ABCG2) in an inward-facing conformation

M. F. Rosenberg, Z. Bikadi, E. Hazai, T. Starborg, L. Kelley, N. E. Chayen, R. C. Ford and Q. Mao

Synopsis: The first three-dimensional structure of human ABCG2 in the absence of nucleotides and transported substrates has been determined at 2.0 nm resolution. In this state, ABCG2 is in an inward-facing conformation.

Accepted 1 June 2015

Structural evidence for asymmetric ligand binding to transthyretin

M. Cianci, C. Folli, F. Zonta, P. Florio, R. Berni and G. Zanotti

Synopsis: Transthyretin represents a notable example of an amyloidogenic protein which undergoes misfolding, leading to a degenerative disease known as amyloidosis. Evidence is provided for significant conformational differences between the two thyroxine binding sites in solution, consistent with an asymmetric ligand-binding pattern. Rationalization of the structural basis of the observed asymmetry will aid in the design of new drugs effective as transthyretin stabilizers, with the prospect of their use in the pharmacological therapy of transthyretin amyloidosis.

Accepted 31 May 2015

The quaternary structure of the eukaryotic DNA replication proteins Sld7 and Sld3

H. Itou, Y. Shirakihara and H. Araki

Synopsis: Crystal structures of the eukaryotic DNA replication initiator Sld7 in complex with Sld3 from yeasts were determined. The quaternary structure of the Sld3-Sld7 complex appears to be suitable to activate two helicase molecules loaded onto replication origins in a head-to-head manner.

Accepted 29 May 2015

Combining `dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography

M. Gelin, V. Delfosse, F. Allemand, F. Hoh, Y. Sallaz-Damaz, M. Pirocchi, W. Bourguet, J.-L. Ferrer, G. Labesse and J.-F. Guichou

Synopsis: In order to accelerate ligand screening using X-ray crystallography, the combination of in situ diffraction with pre-coating of 96-well crystallization plates using a DMSO stock solution of putative ligands before performing protein crystallization is proposed.

Accepted 28 May 2015

Structure of the DNA-binding domain of the response regulator SaeR from Staphylococcus aureus

X. Fan, X. Zhang, Y. Zhu, L. Niu, M. Teng, B. Sun and X. Li

Synopsis: SaeR can bind to P1 promoter DNA using the canonical winged helix-turn-helix module.

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 10 Met) by sulfur SAD phasing at 3.1 Å resolution while overcoming crystal twinning.

Accepted 26 May 2015

Structure of the green fluorescent protein NowGFP with an anionic tryptophan-based chromophore

V. Z. Pletnev, N. V. Pletneva, K. S. Sarkisyan, A. S. Mishin, K. A. Lukyanov, E. A. Goryacheva, R. H. Ziganshin, Z. Dauter and S. Pletnev

Synopsis: The three-dimensional structure of the green fluorescent protein NowGFP (a successor to Cerulean) with an anionic tryptophan-based chromophore and that of the photoconverted form NowGFP_conv are reported. The relationship between structure and photophysical characteristics is investigated.

Accepted 22 May 2015

Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism

A. M. V. Murthy, S. Mathivanan, S. Chittori, H. S. Savithri and M. R. N. Murthy

Accepted 20 May 2015

Structural and adhesive properties of the long polar fimbriae protein LpfD from adherent-invasive Escherichia coli

F. Coppens, J. Iyyathurai, S. Ruer, A. Fioravanti, J. Taganna, L. Vereecke, H. De Greve and H. Remaut

Synopsis: The LpfD protein represents the tip adhesin of enterobacteriaceal long polar fimbriae (LPF), and LpfD from the adherent invasive E. coli strain LF82 directs LPF binding towards the intestinal epithelium and underlying tissue.

Accepted 18 May 2015

Structural basis of Deerpox virus-mediated inhibition of apoptosis

D. R. Burton, S. Caria, B. Marshall, M. Barry and M. Kvansakul

Synopsis: Deerpox virus employs the cell-death inhibitor DPV022 to prevent premature host cell death by engaging pro-death Bcl-2 proteins via two independent ligand-binding sites as part of a domain-swapped Bcl-2 fold.

Accepted 27 April 2015

Detection of trans-cis flips and peptide-plane flips in protein structures

W. G. Touw, R. P. Joosten and G. Vriend

Synopsis: A method is presented to detect peptide bonds that need either a trans-cis flip or a peptide-plane flip.

Accepted 22 April 2015

Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens

A. Chaikuad, S. Knapp and F. von Delft

Accepted 18 April 2015

A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens

C. Y. Koh, L. Kallur Siddaramaiah, R. M. Ranade, J. Nguyen, T. Jian, Z. Zhang, J. R. Gillespie, F. S. Buckner, C. L. M. J. Verlinde, E. Fan and W. G. J. Hol

Synopsis: A crystallographic cocktail screening campaign against 680 fragments revealed a binding hotspot in the structure of T. cruzi histidyl-tRNA synthetase.

Accepted 15 April 2015

Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles

A. H. Van Benschoten, P. V. Afonine, T. C. Terwilliger, M. E. Wall, C. J. Jackson, N. K. Sauter, P. D. Adams, A. Urzhumtsev and J. S. Fraser

Synopsis: A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different translation-libration-screw refinement strategies produce unique diffuse intensity patterns.

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