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 28 August 2014

A Novel Member of Glycoside Hydrolase Family 30 Subfamily 8 with Altered Substrate Specificity

F. J. St John, D. Dietrich, C. Crooks, E. Pozharski, J. M. González, E. Bales, K. Smith and J. C. Hurlbert

Accepted 27 August 2014

Covering the complete proteomes with X-ray structures - a current snapshot

M. J. Mizianty, X. Fan, J. Yan, E. Chalmers, C. Woloschuk, A. Joachimiak and L. Kurgan

Synopsis: We estimate current and attainable coverage by the X-ray structures of proteins and their functions on scale of the "protein universe". We performed detailed analysis of coverage across nearly 2,000 proteomes in all superkingdoms of life and functional annotations, and with particular focus on human proteome and the family of GPCR proteins.

Accepted 27 August 2014

Ligand-dependent active-site closure revealed in the crystal structure of Mycobacterium tuberculosis MenB complexed with product analogs

H. Song, H. P. Sung, Y. S. Tse, M. Jiang and Z. Guo

Accepted 26 August 2014

Structure, mechanism and ensemble formation of the Alkylhydroperoxide Reductase subunits AhpC and AhpF from Escherichia coli

P. Vinh Dip, N. Kamariah, M. S. Subramanian Manimekalai, W. Nartey, A. Manikkoth Balakrishna, F. Eisenhaber, B. Eisenhaber and G. Grüber

Accepted 25 August 2014

Enzyme-substrate complex structures of CYP154C5 shed light on its mode of highly selective steroid hydroxylation

K. Herzog, P. Bracco, A. Onoda, T. Hayashi, K. Hoffmann and A. Schallmey

Synopsis: Four enzyme-substrate complex structures of CYP154C5 from Nocardia farcinica with steroids pregnenolone, progesterone, androstenedione and testosterone bound in the enzyme's active site are reported revealing structural determinants for CYP154C5's high regio- and stereoselectivity in steroid hydroxylation.

Accepted 21 August 2014

Structure of mouse muskelin discoidin domain and biochemical characterization of its self-association

K.-H. Kim, S. K. Hong, K. Y. Hwang and E. E. Kim

Synopsis: The structure of discoidin domain from mouse muskelin is determined and an analysis on the inter-domain interaction suggests the mechanism for self-association.

Accepted 18 August 2014

Structural basis for the recognition of muramyltripeptide by Helicobacter pylori Csd4, a D,L-carboxypeptidase controlling the helical cell shape

H. S. Kim, J. Kim, H. N. Im, D. R. An, M. Lee, D. Hesek, S. Mobashery, J. Y. Kim, K. Cho, H. J. Yoon, B. W. Han, B. I. Lee and S. W. Suh

Synopsis: H. pylori Csd4 (HP1075), together with other peptidoglycan hydrolases, plays an important role in determining the helical cell shape. Its crystal structure has been determined in three different forms.

Accepted 15 August 2014

Structure-specificity relationships in Abp, a GH27 [beta]-L-arabinopyranosidase from Geobacillus stearothermophilus

S. Lansky, R. Salama, H. V. Solomon, H. Feinberg, H. Belrhali, Y. Shoham and G. Shoham

Synopsis: The three-dimensional structure of the GH27 arabinopyranosidase (Abp) from Geobacillus stearothermophilus T6 has been determined by molecular replacement, leading to full structural analysis of Abp-WT (at 2.28 Å resolution) and its catalytic mutant Abp-D197A with (2.20 Å) and without (2.30 Å) a bound L-arabinose product. The structures demonstrate that Abp is a tetramer built of two pincer-like dimers, as also confirmed by SAXS.

Accepted 13 August 2014

Small angle neutron scattering reveals the assembling mode and oligomeric architecture of TET, a large, dodecameric aminopeptidase

A. Appolaire, E. Girard, M. Colombo, M. A. Durá, M. Moulin, M. Härtlein, B. Franzetti and F. Gabel

Synopsis: The present work illustrates that small angle neutron scattering, deuteration and contrast variation, combined with in vitro particle reconstruction, constitutes a very efficient approach to determine subunit architectures in large, symmetric protein complexes. In the case of the 468-kDa hetero-dodecameric TET peptidase machine, it allowed us to demonstrate that the assembling of the 12 subunits is a highly controlled process and represents a way to optimize the enzyme's catalytic efficiency.

Accepted 7 August 2014

Anthrax Toxin Lethal Factor Domain 3 is Highly Mobile and Responsive to Ligand Binding

K. M. Maize, E. K. Kurbanov, T. De La Mora-Rey, T. W. Geders, D.-J. Hwang, M. A. Walters, R. Johnson, E. A. Amin and B. C. Finzel

Accepted 7 August 2014

The Structural Basis of Urea-Induced Protein Unfolding in Beta-catenin

C. Wang, Z. Chen, X. Hong, F. Ning, H. Liu, J. Zang, X. Yan, J. Kemp, C. A. Musselman, T. G. Kutateladze, R. Zhao, Jiang and G. Zhang

Accepted 6 August 2014

Collaborative Computational Project for Electron cryo-Microscopy

C. Wood, T. Burnley, A. Patwardhan, S. Scheres, M. Topf, A. Roseman and M. Winn

Synopsis: The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) is a new initiative for the structural biology community, following the success of CCP4 for macromolecular crystallography. We report progress in supporting users and developers of cryoEM software.

Accepted 1 August 2014

Temperature-Dependent Radiation Sensitivity and Order of 70S Ribosome Crystals

M. Warkentin, J. B. Hopkins, J. B. Haber, G. Blaha and R. E. Thorne

Synopsis: The rate of global radiation damage to 70S ribosome crystals has been measured at 100 K, 180 K, and 300 K. At 100 K and 300 K, damage rates are comparable to and much larger than those of model proteins, respectively. Larger damage rates at 300 K cannot explain the dramatically higher diffraction quality observed at 100 K.

Accepted 1 August 2014

Human insulin analogues modified at B26 site reveal hormone conformation undetected in the receptor complex

L. Záková, E. Kletvíková, M. Lepsík, M. Collinsová, C. J. Watson, J. P. Turkenburg, J. Jirácek and A. M. Brzozowski

Accepted 31 July 2014

Crystallographic Study of the EptC Phosphoethanolamine Transferase Required for Polymyxin Resistance and Motility in Campylobacter jejuni

C. D. Fage, D. B. Brown, J. M. Boll, A. T. Keatinge-Clay and M. S. Trent

Synopsis: The Campylobacter jejuni phosphoethanolamine transferase EptC functions in antibacterial resistance, motility, and host intestinal colonization. In this study, we report the three-dimensional structure of the catalytic domain of EptC in a covalent phospho-enzyme intermediate state. EptC active-site mutant strains of C. jejuni demonstrate the potential for EptC enzyme inhibitors.

Accepted 31 July 2014

Insights into the Binding of PARP Inhibitors to the Catalytic Domain of Human Tankyrase-2

W. Qiu, R. Lam, V. Oleksandr, V. Romanov, R. Gordon, S. Gebremeskel, J. Vodsedalek, C. Thompson, I. Beletskaya, K. P. Battaile, E. F. Pai, R. Rottapel and N. Y. Chirgadze

Accepted 31 July 2014

Structure of the Bifunctional Aminoglycoside Resistance Enzyme AAC(6')-Ie-APH(2")-Ia Revealed by Crystallographic and Small-Angle X-ray Scattering Analysis

C. A. Smith, M. Toth, T. M. Weiss, H. Frase and S. B. Vakulenko

Synopsis: The X-ray structure of the N-terminal acetyltransferase domain (AAC(6')-Ie) of the bifunctional antibiotic resistance enzyme, AAC(6')-Ie-APH(2")-Ia, has been determined as a ternary kanamycin/coenzyme-A complex. X-ray structures of the isolated AAC(6')-Ie and APH(2")-Ia domains, combined with small-angle X-ray scattering (SAXS) data, allow for the determination of the structural architecture of the full-length bifunctional enzyme in solution.

Accepted 30 July 2014

Using textons to rank crystallization droplets by the likely presence of crystals

J. T. Ng, C. Dekker, M. Kroemer, M. Osborne and F. von Delft

Synopsis: A robust and transferable algorithm is presented to objectively describe and rank robotically captured images of crystallization droplets according to their likelihood of crystalline behaviour for efficient and accurate identification of successful crystallization.

Accepted 30 July 2014

Use of massively multiple merged data for low-resolution S-SAD phasing and refinement of flavivirus NS1

D. L. Akey, W. C. Brown, J. R. Konwerski, C. M. Ogata and J. L. Smith

Synopsis: High-multiplicity data were used to solve the West Nile virus NS1 structure by S-SAD and for the extension of useable resolution for refinement.

Accepted 28 July 2014

Structure of archaerhodopsin-2 at 1.8 Å resolution

T. Kouyama, R. Fujii, S. Kanada, T. Nakanishi, S. K. Chan and M. Murakami

Accepted 26 July 2014

A case study on the treatment of protein SIRAS data

D. Yao, T. Zhang, Y. He, P. Han, M. Cherney, Y. Gu, M. Cygler and H. Fan

Synopsis: A case study on the treatment of SIRAS data using the originally unknown protein LegC3N is described. An iterative direct-method-based treatment was proposed that led to improved results in this particular test case.

Accepted 23 July 2014

Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications

H.-J. Chiu, J. C. Grant, C. L. Farr, L. Jaroszewski, M. W. Knuth, M. D. Miller, M.-A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley and I. A. Wilson

Synopsis: The crystal structure of arabinose-5-phosphate isomerase from B. fragilis NCTC 9343 in complex with an endogenous ligand, CMP-Kdo, is described. Structural and sequence comparisons suggest highly conserved functional residues in the active site that could be targeted for antibacterial drug design.

Accepted 23 July 2014

Continuous mutual improvement of macromolecular structure models in the PDB and X-ray crystallographic software: the dual role of deposited experimental data

T. C. Terwilliger and G. Bricogne

Synopsis: Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible.

Accepted 23 July 2014

New methods for indexing multi-lattice diffraction data

R. J. Gildea, D. G. Waterman, J. M. Parkhurst, D. Axford, G. Sutton, D. I. Stuart, N. K. Sauter, G. Evans and G. Winter

Synopsis: A new indexing method is presented which is capable of indexing multiple crystal lattices from narrow wedges of data. The efficacy of this method is demonstrated with both semi-synthetic multi-lattice data and real multi-lattice data recorded from microcrystals of ~1 µm in size.

Accepted 23 July 2014

Structures of human constitutive nitric oxide synthases

H. Li, J. Jamal, C. Plaza, S. H. Pineda, G. Chreifi, Q. Jing, M. A. Cinelli, R. B. Silverman and T. L. Poulos

Accepted 21 July 2014

Visualization of a substrate-induced productive conformation of the catalytic triad of the Neisseria meningitidis peptidoglycan O-acetylesterase reveals mechanistic conservation in SGNH esterase family members

A. H. Williams, F. J. Veyrier, M. Bonis, Y. Michaud, B. Raynal, M.-K. Taha, S. W. White, A. Haouz and I. G. Boneca

Accepted 18 July 2014

Memprot: A program to model the detergent corona around a membrane protein, based on SEC-SAXS data

A. Koutsioubas and J. Pérez

Accepted 17 July 2014

Protein-Ligand interactions investigated by Thermal Shift Assays (TSA) and Dual Polarization Interferometry (DPI)

M. K. Grøftehauge, N. R. Hajizadeh, M. J. Swann and E. Pohl

Synopsis: The biophysical characterization of protein-ligand interactions in solution by techniques such as thermal shift assay, or on surfaces using for example Dual Polarization Interferometry, plays an increasingly important role to complement crystal structure determinations.

Accepted 17 July 2014

Crystal structure and functional implications of LprF from Mycobacterium tuberculosis and M. bovis

J.-S. Kim, L. Jiao, J.-I. Oh, N.-C. Ha and Y.-H. Kim

Accepted 16 July 2014

The structure of a tetrameric [alpha]-carbonic anhydrase from Thermovibrio ammonificans reveals a core formed around intermolecular disulfides that contribute to its thermostability

P. James, M. N. Isupov, C. Sayer, V. Saneei, S. Berg, M. Lioliou, H. K. Kotlar and J. A. Littlechild

Synopsis: The thermostability of the [alpha]-carbonic anhydrase from the thermophilic bacterium T. ammonificans is shown to depend on the formation of intrasubunit disulfide bonds and a unique intersubunit disulfide/lysine core at the centre of the tetrameric molecule. Unlike most [alpha]-carbonic anhydrases, this enzyme does not show esterase activity towards p-nitrophenyl acetate, which is proposed to be owing to its increased structural rigidity.

Accepted 14 July 2014

Metrics for comparison of crystallographic maps

A. Urzhumtsev, P. V. Afonine, V. Y. Lunin, T. C. Terwilliger and P. D. Adams

Synopsis: Rank scaling of Fourier syntheses leads to new tools for the comparison of crystallographic contour maps. The new metrics are in better agreement with a visual map analysis than the conventional map correlation coefficient.

Accepted 12 July 2014

Conformation-independent structural comparison of macromolecules with ProSMART

R. A. Nicholls, M. Fischer, S. McNicholas and G. N. Murshudov

Synopsis: The Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed to allow local comparative structural analyses independent of the global conformations and sequence homology of the compared macromolecules. This allows quick and intuitive visualization of the conservation of backbone and side-chain conformations, providing complementary information to existing methods.

Accepted 11 July 2014

Operation of the Australian Store.Synchrotron for macromolecular crystallography

G. R. Meyer, D. Aragão, N. J. Mudie, T. T. Caradoc-Davies, S. McGowan, P. J. Bertling, D. Groenewegen, S. M. Quenette, C. S. Bond, A. M. Buckle and S. Androulakis

Accepted 10 July 2014

Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease

C. Shao, C. Wang and J. Zang

Synopsis: The crystal structure of PvuRts1I was determined and a 5-hydroxymethylcytosine-binding pocket was identified in the SRA-like domain. Enzyme variants were engineered to assist in hydroxymethylome mapping based on the crystal structure of PvuRts1I.

Accepted 8 July 2014

A new family of [beta]-helix proteins with similarities to the polysaccharide lyases

D. W. Close, S. D'Angelo and A. R. M. Bradbury

Synopsis: Cthe_2159 is a member of a domain of unknown function) family (DUF4353 and was identified from the C. thermocellum genome by its ability to bind cellulose. The structure was determined using gadolinium SAD phasing and shows structural features that are highly similar to some polysaccharide lyase families.

Accepted 6 July 2014

The structure of allophycocyanin B from Synechocystis PCC 6803 reveals the structural basis for the extreme redshift of the terminal emitter in phycobilisomes

P.-P. Peng, L.-L. Dong, Y.-F. Sun, X.-L. Zeng, W.-L. Ding, H. Scheer, X. Yang and K.-H. Zhao

Accepted 6 July 2014

Solving the RNA polymerase I structural puzzle

M. Moreno-Morcillo, N. M. I. Taylor, T. Gruene, P. Legrand, U. J. Rashid, F. M. Ruiz, U. Steuerwald, C. W. Müller and C. Fernández-Tornero

Synopsis: Details of the RNA polymerase I crystal structure determination provide a framework for solution of the structures of other multi-subunit complexes. Simple crystallographic experiments are described to extract relevant biological information such as the location of the enzyme active site.

Accepted 30 June 2014

Structure of Rot, a global regulator of virulence genes in Staphylococcus aureus

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

Synopsis: The crystal structure of Rot shows a unique pattern of dimerization that differs from that of other SarA homologues.

Accepted 29 June 2014

Crystallographic analysis and biochemical applications of a novel penicillin-binding protein/[beta]-lactamase homologue from a metagenomic library

T. D. Ngo, B. H. Ryu, H. Ju, E. J. Jang, K. K. Kim and T. D. Kim

Synopsis: The crystal structure of Est-Y29, a metagenomic homologue of the penicillin-binding protein/[beta]-lactamase family, was determined at 1.70 Å resolution. The biochemical properties of Est-Y29 were also investigated for potential biotechnological applications.

Accepted 27 June 2014

In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF

D. von Stetten, T. Giraud, P. Carpentier, F. Sever, M. Terrien, F. Dobias, D. H. Juers, D. Flot, C. Mueller-Dieckmann, G. A. Leonard, D. de Sanctis and A. Royant

Synopsis: The current version of the in crystallo optical spectroscopy facility Cryobench of the ESRF is presented. The diverse experiments that can be performed at the Cryobench are also reviewed.

Accepted 26 June 2014

Challenges and solutions for the analysis of in situ, in crystallo micro-spectrophotometric data

F. S. N. Dworkowski, M. A. Hough, G. Pompidor and M. R. Fuchs

Synopsis: We describe why the analysis of optical absorption and Raman spectroscopic data measured from protein crystals is particularly challenging and how the SLS-APE software toolbox supports scientists in dealing with such data.

Accepted 26 June 2014

Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP

R. Keegan, A. Lebedev, P. Erskine, J. Guo, S. P. Wood, D. J. Hopper, S. E. J. Rigby and J. B. Cooper

Synopsis: The first X-ray structure of a 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP at a resolution of 2.2 Å is reported. This structure establishes that the enzyme adopts the cupin-fold, forming compact dimers with a pronounced hydrophobic interface between the monomers. Each monomer possesses a catalytic ferrous iron that is coordinated by three histidines (76, 78 and 114) and an additional ligand which has been putatively assigned as a carbonate, although formate and acetate are possibilities.

Accepted 23 June 2014

Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the program Zanuda

A. A. Lebedev and M. N. Isupov

Synopsis: Pseudo-symmetry, which is common in macromolecular crystals, may result in incorrect space-group assignment that remains unnoticed until the advanced stages of refinement. The program Zanuda has been developed to automate space-group assignment and validation.

Accepted 23 June 2014

Anchoring protein crystals to mounting loops with hydrogel using inkjet technology

A. Shinoda, Y. Tanaka, M. Yao and I. Tanaka

Accepted 13 June 2014

Uniqueness of models from small angle scattering data: the impact of a hydration shell and complementary NMR restraints

H. S. Kim and F. Gabel

Synopsis: A review and discussion of the potentialities and limitations of bio-macromolecular modelling of small angle scattering data with a focus on the impact of complementary NMR restraints and a hydration shell.

Accepted 12 June 2014

Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening

C. M. Cuttitta, D. L. Ericson, A. Scalia, C. G. Roessler, E. Teplitsky, K. Joshi, O. Campos, R. Agarwal, M. Allaire, A. M. Orville, R. M. Sweet and A. S. Soares

Accepted 8 June 2014

Multi-crystal native SAD analysis at 6 keV

Q. Liu, Y. Guo, Y. Chang, Z. Cai, Z. Assur, F. Mancia, M. I. Greene and W. A. Hendrickson

Synopsis: Anomalous diffraction signals may be routinely enhanced for native-SAD analysis by merging multi-crystal data sets at 6 keV.

Accepted 5 June 2014

Insights into the relationship between the haem-binding pocket and the redox potential of c6 cytochromes: four atomic resolution structures of c6 and c6-like proteins from Synechococcus sp. PCC 7002

W. Bialek, S. Krzywda, P. Zatwarnicki, M. Jaskolski, P. Kolesinski and A. Szczepaniak

Synopsis: Atomic resolution structures of cytochromes c6 and c6C from Synechococcus sp. PCC 7002 as well as their haem-pocket point mutants are presented. The biophysical and structural properties of these proteins have been characterized with particular focus on the relationship between the structure of the haem-binding pocket and the redox potential.

Accepted 12 May 2014

The accurate assessment of small-angle X-ray scattering data

T. D. Grant, J. R. Luft, L. G. Carter, T. Matsui, T. M. Weiss, A. Martel and E. H. Snell

Synopsis: A set of quantitative techniques is suggested for assessing SAXS data quality. These are applied in the form of a script, SAXStats, to a test set of 27 proteins showing that these techniques are more sensitive than manual assessment of data quality.

Accepted 7 May 2014

Experimental phasing for structure determination using membrane protein crystals grown by the lipid cubic phase method

D. Li, V. Pye and M. Caffrey

Synopsis: Very little information is available in the literature concerning experimental, heavy atom phasing of membrane protein structures where the crystals have been grown using the lipid cubic phase (in meso) method. In this paper, pre-labelling, co-crystallization, soaking, site-specific mercury binding to genetically engineered single cysteine mutants, and seleno-methionine labelling as applied to an integral membrane kinase crystallized in meso are described. An assay to assess cysteine accessibility for mercury labelling of membrane proteins is introduced.

Accepted 7 May 2014

Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

H. Zhao and P. Schuck

Synopsis: Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of stoichiometry, affinity, and cooperativity of multi-site interactions. We review principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT, describe their complementarity in GMMA, and present a new GMMA simulation tool set in SEDPHAT.

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