Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 5 (May 2013)


Including articles from the Integrated Software for Integrative Structural Biology workshop edited by Chris Morris


[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: A Chi60 chitinase molecule (p. 821) attached to the surface of chitin via its chitin-binding domain. The structure of Chi60 is crystallographic. The surface of chitin has been generated by expanding the known crystal structure of an N-acetyl glucosamine oligomer by the application of crystallographic symmetry. The association of Chi60 with the chitin surface is hypothetical. The inset shows the three surface tryptophan side chains of the chitin-binding domain in their hypothetical interaction with the chitin surface.

integrative structural biology


 

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Acta Cryst. (2013). D69, 681-682  [ doi:10.1107/S090744491300276X ]

Towards a structural biology work bench

C. Morris

Synopsis: The trends to investigate larger complexes and more transient phenomena pose some challenges to software developers.

Online 19 April 2013


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Acta Cryst. (2013). D69, 683-694  [ doi:10.1107/S0907444913007063 ]

On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys

E. Karaca and A. M. J. J. Bonvin

Synopsis: In this research, the usefulness of low-resolution shape data for scoring docking decoys is explored. Within this context, a new scoring function is introduced that combines the regular HADDOCK score with either small-angle X-ray scattering or collision cross-section data.

Online 19 April 2013


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Acta Cryst. (2013). D69, 695-700  [ doi:10.1107/S0907444913007038 ]

On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy

R. Marabini, J. R. Macias, J. Vargas, A. Quintana, C. O. S. Sorzano and J. M. Carazo

Synopsis: This work describes three developments promoting integrative biology, standardization and workflow processing, namely PeppeR, the EMX initiative and Scipion.

Online 19 April 2013


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Acta Cryst. (2013). D69, 701-709  [ doi:10.1107/S0907444913007051 ]

OpenStructure: an integrated software framework for computational structural biology

M. Biasini, T. Schmidt, S. Bienert, V. Mariani, G. Studer, J. Haas, N. Johner, A. D. Schenk, A. Philippsen and T. Schwede

Synopsis: Current developments in the computational structural biology framework OpenStructure are presented.

Online 19 April 2013


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Acta Cryst. (2013). D69, 710-721  [ doi:10.1107/S0907444913001157 ]

The role of structural bioinformatics resources in the era of integrative structural biology

A. Gutmanas, T. J. Oldfield, A. Patwardhan, S. Sen, S. Velankar and G. J. Kleywegt

Synopsis: The integration of structural data on atomistic to cellular scales with genetic, taxonomic and functional information is discussed. The challenges to the PDB and EMDB archives and some pertinent developments at PDBe to address these are discussed.

Online 19 April 2013


research papers


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Acta Cryst. (2013). D69, 722-734  [ doi:10.1107/S0907444913001182 ]

The structure of cardiac troponin C regulatory domain with bound Cd2+ reveals a closed conformation and unique ion coordination

X. L. Zhang, G. F. Tibbits and M. Paetzel

Synopsis: A 1.4 Å resolution crystal structure of wild-type human cardiac troponin C regulatory domain (cNTnC) in complex with Cd2+ is compared with structures of other EF-hand containing proteins that have been cocrystallized with Cd2+. Structures of cNTnC with disease-related mutations L29Q and NIQD (D2N/V28I/L29Q/G30G) are also determined.

PDB references: 3swb, 3sd6, 4gje, 4gjf and 4gjg

Online 11 April 2013


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Acta Cryst. (2013). D69, 735-746  [ doi:10.1107/S0907444913001236 ]

Structural and functional characterization of HP0377, a thioredoxin-fold protein from Helicobacter pylori

J. Y. Yoon, J. Kim, D. R. An, S. J. Lee, H. S. Kim, H. N. Im, H.-J. Yoon, J. Y. Kim, S.-J. Kim, B. W. Han and S. W. Suh

Synopsis: The results of structural and functional characterizations of H. pylori HP0377, a thioredoxin-fold protein, are reported. HP0377 can reduce apocytochrome c553 (HP1227) and forms a covalent complex with a putative L,D-transpeptidase (HP0518) via a disulfide bond, suggesting that HP0377 may serve multiple functions as a reductase in H. pylori.

PDB references: 4fyb and 4fyc

Online 11 April 2013


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Acta Cryst. (2013). D69, 747-755  [ doi:10.1107/S0907444913001315 ]

Mechanism for controlling the monomer-dimer conversion of SARS coronavirus main protease

C.-G. Wu, S.-C. Cheng, S.-C. Chen, J.-Y. Li, Y.-H. Fang, Y.-H. Chen and C.-Y. Chou

Synopsis: The crystal structure of the dimeric R298A mutant of SARS-CoV Mpro offers insights into the molecular mechanism controlling monomer-dimer conversion during the process of Mpro maturation.

PDB reference: 4hi3

Online 11 April 2013


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Acta Cryst. (2013). D69, 756-766  [ doi:10.1107/S0907444913001522 ]

Atomic resolution structures of the c-Src SH3 domain in complex with two high-affinity peptides from classes I and II

J. Bacarizo and A. Camara-Artigas

Synopsis: The first crystallographic structures of the c-Src SH3 domain in complex with two different high-affinity peptides have been solved at atomic resolution.

PDB references: 4hvu, 4hvv and 4hvw

Online 11 April 2013


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Acta Cryst. (2013). D69, 767-773  [ doi:10.1107/S0907444913001546 ]

The 1.6 Å resolution structure of a FRET-optimized Cerulean fluorescent protein

J. L. Watkins, H. Kim, M. L. Markwardt, L. Chen, R. Fromme, M. A. Rizzo and R. M. Wachter

Synopsis: The high resolution X-ray structure of the cyan fluorescent protein mCerulean3 demonstrates that different combinations of correlated residue substitutions can provide near optimum quantum yield values for fluorescence.

PDB reference: 4en1

Online 11 April 2013


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Acta Cryst. (2013). D69, 774-784  [ doi:10.1107/S0907444913001558 ]

The structure of the caspase recruitment domain of BinCARD reveals that all three cysteines can be oxidized

K.-E. Chen, A. A. Richards, T. T. Caradoc-Davies, P. R. Vajjhala, G. Robin, L. H. L. Lua, J. M. Hill, K. Schroder, M. J. Sweet, S. Kellie, B. Kobe and J. Martin

Synopsis: The mitochondrial localization of BinCARD and the susceptibility to oxidation of all three of its cysteines suggest the possibility of a role in redox regulation.

PDB references: 4dwn and 4fh0

Online 11 April 2013


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Acta Cryst. (2013). D69, 785-795  [ doi:10.1107/S0907444913001923 ]

Structural analysis of malaria-parasite lysyl-tRNA synthetase provides a platform for drug development

S. Khan, A. Garg, N. Camacho, J. Van Rooyen, A. Kumar Pole, H. Belrhali, L. Ribas de Pouplana, V. Sharma and A. Sharma

Synopsis: Crystal structure of malaria parasite lysyl tRNA synthetase provides basis for drug development.

PDB reference: 4h02

Online 11 April 2013


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Acta Cryst. (2013). D69, 796-803  [ doi:10.1107/S0907444913001984 ]

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

Y. Tsai, S. E. McPhillips, A. González, T. M. McPhillips, D. Zinn, A. E. Cohen, M. D. Feese, D. Bushnell, T. Tiefenbrunn, C. D. Stout, B. Ludaescher, B. Hedman, K. O. Hodgson and S. M. Soltis

Synopsis: New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples.

Online 11 April 2013


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Acta Cryst. (2013). D69, 804-811  [ doi:10.1107/S0907444913002096 ]

Structural basis of L-phosphoserine binding to Bacillus alcalophilus phosphoserine aminotransferase

P. Battula, A. P. Dubnovitsky and A. C. Papageorgiou

Synopsis: The structures of Bacillus alcalophilus phosphoserine aminotransferase in the presence or absence of L-phosphoserine were determined at 1.5 and 1.6 Å resolution, respectively. Structural comparison revealed local conformational changes and the formation of a tight phosphate-binding site upon L-phosphoserine binding.

PDB references: 4azj and 4azk

Online 11 April 2013


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Acta Cryst. (2013). D69, 812-820  [ doi:10.1107/S0907444913002102 ]

Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins

V. A. Meshcheryakov, A. Kitao, H. Matsunami and F. A. Samatey

Synopsis: Crystal structures of the cytoplasmic domain of FlhB from S. typhimurium and A. aeolicus were solved at 2.45 and 2.55 Å resolution, respectively. The deletion of a short loop in the cytoplasmic domain of Salmonella FlhB completely abolishes secretion by the type III secretion system. A molecular-dynamics simulation shows that the deletion of the loop affects the flexibility of a linker between the transmembrane and cytoplasmic domains of FlhB.

PDB references: 3b0z and 3b1s

Online 11 April 2013


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Acta Cryst. (2013). D69, 821-829  [ doi:10.1107/S0907444913002011 ]

Structure of a complete four-domain chitinase from Moritella marina, a marine psychrophilic bacterium

P. H. Malecki, J. E. Raczynska, C. E. Vorgias and W. Rypniewski

Synopsis: Chitinase from a cold-adapted bacterium has been examined in the unliganded form and in complexes with the reaction intermediate and the reaction product. The structure, which consists of four linearly arranged domains, has been examined for features responsible for the activity, specificity and adaptation to low temperatures of the enzyme.

PDB references: 4hmc, 4hmd and 4hme

Online 11 April 2013


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Acta Cryst. (2013). D69, 830-837  [ doi:10.1107/S0907444913002023 ]

The structures of Arabidopsis Deg5 and Deg8 reveal new insights into HtrA proteases

W. Sun, F. Gao, H. Fan, X. Shan, R. Sun, L. Liu and W. Gong

Synopsis: The crystal structures of Arabidopsis Deg5 and Deg8 have been determined to resolutions of 2.6 and 2.0 Å, respectively, revealing novel structural features of HtrA proteases.

PDB references: 4ic5 and 4ic6

Online 11 April 2013


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Acta Cryst. (2013). D69, 838-842  [ doi:10.1107/S0907444913002448 ]

Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser

T. R. M. Barends, L. Foucar, R. L. Shoeman, S. Bari, S. W. Epp, R. Hartmann, G. Hauser, M. Huth, C. Kieser, L. Lomb, K. Motomura, K. Nagaya, C. Schmidt, R. Strecker, D. Anielski, R. Boll, B. Erk, H. Fukuzawa, E. Hartmann, T. Hatsui, P. Holl, Y. Inubushi, T. Ishikawa, S. Kassemeyer, C. Kaiser, F. Koeck, N. Kunishima, M. Kurka, D. Rolles, B. Rudek, A. Rudenko, T. Sato, C.-D. Schroeter, H. Soltau, L. Strueder, T. Tanaka, T. Togashi, K. Tono, J. Ullrich, S. Yase, S. Wada, M. Yao, M. Yabashi, K. Ueda and I. Schlichting

Synopsis: Analysis of serial femtosecond crystallographic data measured using the SACLA free-electron laser at RIKEN Harima shows the weak anomalous signal from naturally occurring S atoms in a protein.

Online 11 April 2013


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Acta Cryst. (2013). D69, 843-851  [ doi:10.1107/S0907444913002746 ]

Towards protein-crystal centering using second-harmonic generation (SHG) microscopy

D. J. Kissick, C. M. Dettmar, M. Becker, A. M. Mulichak, V. Cherezov, S. L. Ginell, K. P. Battaile, L. J. Keefe, R. F. Fischetti and G. J. Simpson

Synopsis: The potential of second-harmonic generation (SHG) microscopy for automated crystal centering to guide synchrotron X-ray diffraction of protein crystals has been explored.

PDB references: 4dc5, 4dc6, 4dc7 and 4dc8

Online 19 April 2013


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Acta Cryst. (2013). D69, 852-859  [ doi:10.1107/S0907444913002734 ]

Imaging protein three-dimensional nanocrystals with cryo-EM

I. Nederlof, Y. W. Li, M. van Heel and J. P. Abrahams

Synopsis: Electron imaging of three-dimensional protein nanocrystals using a Titan Krios electron microscope and a Falcon direct electron detector revealed structural details at higher than 3 Å resolution. Image processing with IMAGIC (cryo-EM single-particle analysis software) could improve the data to beyond 2 Å resolution.

Online 19 April 2013


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Acta Cryst. (2013). D69, 860-865  [ doi:10.1107/S0907444913002771 ]

Effects of cryoprotectants on the structure and thermostability of the human carbonic anhydrase II-acetazolamide complex

M. Aggarwal, C. D. Boone, B. Kondeti, C. Tu, D. N. Silverman and R. McKenna

Synopsis: Here, a case study of the effects of cryoprotectants on the kinetics of carbonic anhydrase II (CA II) and its inhibition by the clinically used inhibitor acetazolamide (AZM) is presented.

PDB references: 3v2j and 3v2m

Online 19 April 2013


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Acta Cryst. (2013). D69, 866-871  [ doi:10.1107/S0907444913002862 ]

Structures of Enterovirus 71 3C proteinase (strain E2004104-TW-CDC) and its complex with rupintrivir

C. Wu, Q. Cai, C. Chen, N. Li, X. Peng, Y. Cai, K. Yin, X. Chen, X. Wang, R. Zhang, L. Liu, S. Chen, J. Li and T. Lin

Synopsis: The crystal structures of Enterovirus 71 3C proteinase and its complex with rupintrivir are reported.

PDB references: 4ghq and 4ght

Online 19 April 2013


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Acta Cryst. (2013). D69, 872-878  [ doi:10.1107/S0907444913002722 ]

On optimal placement of molecules in the unit cell

Z. Dauter

Synopsis: Standard ways for the placement of molecules in the unit cell are proposed.

Online 19 April 2013


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Acta Cryst. (2013). D69, 879-887  [ doi:10.1107/S0907444913002576 ]

The structure of the SBP-Tag-streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits

I. H. Barrette-Ng, S.-C. Wu, W.-M. Tjia, S.-L. Wong and K. K. S. Ng

Synopsis: The structure of the SBP-Tag-streptavidin complex reveals a novel mode of peptide recognition in which a single peptide binds simultaneously to biotin-binding pockets from adjacent subunits of streptavidin. The molecular details of peptide recognition suggest how the SBP-Tag can be further modified to become an even more useful tag for a wider range of biotechnological applications.

PDB reference: 4jo6

Online 19 April 2013


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Acta Cryst. (2013). D69, 888-900  [ doi:10.1107/S0907444913002874 ]

Structural analysis of coniferyl alcohol 9-O-methyltransferase from Linum nodiflorum reveals a novel active-site environment

S. Wolters, M. Neeb, A. Berim, J. Schulze Wischeler, M. Petersen and A. Heine

Synopsis: The de novo structure of coniferyl alcohol 9-O-methyltransferase and ITC measurements suggest a novel binding mode and reaction mechanism in plant small-molecule O-methyltransferases.

PDB references: 4ems, 4e70 and 4evi

Online 19 April 2013


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Acta Cryst. (2013). D69, 901-913  [ doi:10.1107/S0907444913003260 ]

Camel and bovine chymosin: the relationship between their structures and cheese-making properties

J. Langholm Jensen, A. Mølgaard, J.-C. Navarro Poulsen, M. K. Harboe, J. B. Simonsen, A. M. Lorentzen, K. Hjernø, J. M. van den Brink, K. B. Qvist and S. Larsen

Synopsis: Analysis of the crystal structures of the two milk-clotting enzymes bovine and camel chymosin has revealed that the better milk-clotting activity towards bovine milk of camel chymosin compared with bovine chymosin is related to variations in their surface charges and their substrate-binding clefts.

PDB references: 4aa8 and 4aa9

Online 19 April 2013


short communications


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Acta Cryst. (2013). D69, 914-919  [ doi:10.1107/S0907444913001728 ]

Integrated database of information from structural genomics experiments

Y. Asada, M. Sugahara, H. Mizutani, H. Naitow, T. Tanaka, Y. Matsuura, Y. Agari, A. Ebihara, A. Shinkai, S. Kuramitsu, S. Yokoyama, E. Kaminuma, N. Kobayashi, K. Nishikata, S. Shimoyama, T. Toyoda, T. Ishikawa and N. Kunishima

Synopsis: Information from structural genomics experiments has been compiled and published as an integrated database.

Online 19 April 2013


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Acta Cryst. (2013). D69, 920-923  [ doi:10.1107/S0907444913002412 ]

Using high-throughput in situ plate screening to evaluate the effect of dehydration on protein crystals

A. Douangamath, P. Aller, P. Lukacik, J. Sanchez-Weatherby, I. Moraes and J. Brandao-Neto

Synopsis: A novel high-throughput in situ plate-screening procedure is used to assess the effect of dehydration on a membrane-associated protein. In this case the dehydration improved the diffraction quality of the crystal.

Online 19 April 2013


books received


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Acta Cryst. (2013). D69, 924  [ doi:10.1107/S0907444913001856 ]

Visualizing the Invisible: Imaging Techniques for the Structural Biologist

Online 19 April 2013


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