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 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 21 July 2014

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

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 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 Thermovibrio ammonificans is shown to depend on 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 due to its increased structural rigidity.


Accepted 16 July 2014

Deformable Elastic Network Refinement for Low-Resolution Macromolecular Crystallography

G. F. Schröder, M. Levitt and A. T. Brunger

Synopsis: An overview of applications of the deformable elastic network (DEN) refinement method is presented together with recommendations of its optimal usage.


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 comparison 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 compared macromolecules' global conformations and sequence homology. This allows quick and intuitive visualization of the conservation of backbone and side chain conformations, providing information complementary 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 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 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 the domain of unknown function (DUF4353) family 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

Structure of allophycocyanin B from Synechocystis PCC 6803 reveals structural basis for extreme red-shift of 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 to solve 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 differing 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


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 is unnoticed until 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 22 June 2014

The structure of the C-terminal domain of the Zaire ebolavirus nucleoprotein

P. J. Dziubanska, U. Derewenda, J. F. Ellena, D. A. Engel and Z. S. Derewenda

Synopsis: The structure of the C-terminal domain of the Zaire ebolavirus nucleoprotein (NP), encompassing residues 641-739, was determined in two distinct crystal forms. The domain has a novel fold that is distantly related to the [beta]-grasp fold.


Accepted 20 June 2014

Local dynamics of proteins and DNA evaluated from crystallographic B factors

B. Schneider, J.-C. Gelly, A. G. de Brevern and J. Cerný


Accepted 18 June 2014

An evaluation of adhesive sample holders for advanced crystallographic experiments

M. Mazzorana, J. Sanchez-Weatherby, J. Sandy, C. M. C. Lobley and T. Sorensen

Synopsis: Commercially available adhesives have been evaluated for crystal mounting when undertaking complex macromolecular crystallography experiments. Here, their use as tools for advanced sample mounting and cryoprotection is assessed and their suitability for room-temperature data-collection and humidity-control studies is investigated.


Accepted 18 June 2014

Structural insight into arginine methylation by the mouse protein arginine methyltransferase 7: a zinc finger freezes the mimic of the dimeric state into a single active site

V. Cura, N. Troffer-Charlier, J.-M. Wurtz, L. Bonnefond and J. Cavarelli

Synopsis: The crystal structure of full-length PRMT7 from M. musculus refined at 1.7 Å resolution is reported and provides structural clues for the monomethylation of arginine.


Accepted 17 June 2014

Structure of the double-stranded DNA-binding type IV secretion protein TraN from Enterococcus

N. Gössweiner-Mohr, M. Eder, G. Hofer, C. Fercher, K. Arends, R. Birner-Gruenberger, E. Grohmann and W. Keller

Synopsis: The TraN structure shows an internal dimer fold with helix-turn-helix motifs at both ends. The protein is a double-stranded DNA-binding protein that binds upstream of the pIP501 oriT, presumably acting as a type IV secretion-system regulator involved in early steps of conjugative transfer.


Accepted 14 June 2014

A high-throughput colourimetric method for the determination of pH in crystallization screens

J. Kirkwood, J. Wilson, S. O'Keefe and D. Hargreaves

Synopsis: The recorded pH of protein crystallization screens is often inaccurate. Here, a method has been developed for the high-throughput measurement of pH for these screens using an acid-base indicator and a spectrophotometer.


Accepted 13 June 2014

Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination

C.-D. Chen, Y.-C. Huang, H.-L. Chiang, Y.-C. Hsieh, H.-H. Guan, P. Chuankhayan and C.-J. Chen

Synopsis: A novel direct phase-selection method to select optimized phases from the ambiguous phases of a subset of reflections to replace the corresponding initial SAD phases has been developed. With the improved phases, the completeness of built residues of protein molecules is enhanced for efficient structure determination.


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 13 June 2014

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

R. McGreevy, A. Singharoy, Q. Li, J. Zhang, D. Xu, E. Perozo and K. Schulten

Synopsis: A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein.


Accepted 13 June 2014

Expression, crystal structure and cellulase activity of the thermostable cellobiohydrolase Cel7A from the fungus Humicola grisea var. thermoidea

M. Haddad Momeni, F. Goedegebuur, H. Hansson, S. Karkehabadi, G. Askarieh, C. Mitchinson, E. A. Larenas, J. Ståhlberg and M. Sandgren

Synopsis: Cellobiohydrolase Cel7A from H. grisea var. thermoidea showed a 10°C higher Tm and a 75% higher yield than H. jecorina Cel7A in a performance assay at 65°C. The crystal structure at 1.8 Å resolution indicates higher flexibility in tunnel-defining loops and reveals a new loop conformation near the active centre.


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 12 June 2014

Latent and active abPPO4 mushroom tyrosinases cocrystallized with hexatungstotellurate(VI) in a single crystal

S. G. Mauracher, C. Molitor, R. Al-Oweini, U. Kortz and A. Rompel

Synopsis: Mushroom tyrosinase isoform abPPO4 (Agaricus bisporus polyphenol oxidase 4) was crystallized by means of an Anderson-type polyoxometalate. The enzyme crystallized as a heterodimer containing the zymogen (L-TYR; 64 kDa), the 21 kDa smaller activated form (A-TYR) and the polyoxoanion (POM) within one single crystal in a 1:1:1 ratio.


Accepted 12 June 2014

Satellite tobacco mosaic virus refined to 1.4 Å resolution

S. B. Larson, J. S. Day and A. McPherson

Synopsis: The crystal structure of Satellite tobacco mosaic virus (STMV) at 1.4 Å resolution represents the highest resolution and most precise native virus structure, utilizing more than twice as many reflections in refinement as were used for the previous STMV model. New details regarding the multiple ion arrangement on fivefold axes, the disposition of the `free' nucleotide, alternate conformations of amino-acid side chains and the distortion of the capsid from strict icosahedral symmetry have emerged.


Accepted 11 June 2014

Structure of human endonuclease V as an inosine-specific ribonuclease

Z. Zhang, Z. Hao, Z. Wang, Q. Li and W. Xie

Synopsis: A 2.3 Å resolution crystal structure of human EndoV was determined and the structural basis of its unusual substrate specificities was explored.


Accepted 11 June 2014

Mutational and structural study of RipA, a key enzyme in Mycobacterium tuberculosis cell division: evidence for the L-to-D inversion of configuration of the catalytic cysteine

F. Squeglia, A. Ruggiero, M. Romano, L. Vitagliano and R. Berisio


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 27 May 2014

The structure of human interleukin-11 reveals receptor-binding site features and structural differences from interleukin-6

T. L. Putoczki, R. C. J. Dobson and M. D. W. Griffin

Synopsis: Interleukin-11 is a multifunctional member of the interleukin-6 family of cytokines. The crystal structure of human interleukin-11 is reported, providing important structural details of the receptor binding regions and revealing structural differences form the archetypal family member, interlekin-6.


Accepted 13 May 2014

A structural and functional investigation of a novel protein from Mycobacterium smegmatis implicated in mycobacterial macrophage survivability

A. Shahine, D. Littler, R. Brammananath, P. Y. Chan, P. K. Crellin, R. L. Coppel, J. Rossjohn and T. Beddoe

Synopsis: The 2.40 Å resolution crystal structure of MSMEG_5817 revealed structural homology to sterol carrier proteins, suggesting a lipid-transport role in the survival of mycobacteria within host macrophages.


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 9 May 2014

Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis

E. P. Schultz, E. E. Vasquez and W. G. Scott

Synopsis: Comparison of mutant and wild-type hammerhead ribozyme structures reveals active-site structural perturbations consistent with either a general base catalytic mechanism, as previously assumed to be operative in the hammerhead ribozyme, or a specific base catalytic mechanism, which may possess additional explanatory power.


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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