Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 6 (June 2013)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Overall view of the vault structure refined using DEN protocols (p. 1054). A half-vault structure (in dark blue) with one of the 39 MVP copies forming the particle shown in magenta.

research papers


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Acta Cryst. (2013). D69, 925-933  [ doi:10.1107/S0907444913006422 ]

Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms

A. Simonetti, S. Marzi, A. Fabbretti, I. Hazemann, L. Jenner, A. Urzhumtsev, C. O. Gualerzi and B. P. Klaholz

Synopsis: The crystal structures of the eubacterial translation initiation factor 2 in apo form and with bound GDP and GTP reveal conformational changes upon nucleotide binding and hydrolysis, notably of the catalytically important histidine in the switch II region.

PDB references: 4b3x, 4b48 and 4b47

Online 23 April 2013


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Acta Cryst. (2013). D69, 934-945  [ doi:10.1107/S0907444913003624 ]

Structural insight into plant programmed cell death mediated by BAG proteins in Arabidopsis thaliana

S. Fang, L. Li, B. Cui, S. Men, Y. Shen and X. Yang

Synopsis: Crystal structures of the BAG proteins from A. thaliana have been solved at high resolution. Structural and functional data provide evidence of an Hsp70/Hsc70 nucleotide-exchange factor function for these plant BAG proteins.

PDB references: 4hwc, 4hwd, 4hwf, 4hwh and 4hwi

Online 2 May 2013


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Acta Cryst. (2013). D69, 946-959  [ doi:10.1107/S0907444913003454 ]

Resolution of structural heterogeneity in dynamic crystallography

Z. Ren, P. W. Y. Chan, K. Moffat, E. F. Pai, W. E. Royer, V. Srajer and X. Yang

Synopsis: An analytical approach is presented to identify and resolve several distinct structural species dynamically mixed in multiple crystallographic data sets.

Online 2 May 2013


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Acta Cryst. (2013). D69, 960-967  [ doi:10.1107/S0907444913003569 ]

A novel interdomain interface in crystallins: structural characterization of the [beta][gamma]-crystallin from Geodia cydonium at 0.99 Å resolution

A. Vergara, M. Grassi, F. Sica, E. Pizzo, G. D'Alessio, L. Mazzarella and A. Merlino

Synopsis: The X-ray crystal structure of geodin is reported.

PDB reference: 4iau

Online 2 May 2013


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Acta Cryst. (2013). D69, 968-977  [ doi:10.1107/S0907444913003855 ]

Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin

I. Le Trong, V. Chu, Y. Xing, T. P. Lybrand, P. S. Stayton and R. E. Stenkamp

Synopsis: The crystal structures of two circularly permuted streptavidins probe the role of a flexible loop in the tight binding of biotin. Molecular-dynamics calculations for one of the mutants suggests that increased fluctuations in a hydrogen bond between the protein and biotin are associated with cleavage of the binding loop.

PDB references: 4gd9 and 4gda

Online 11 May 2013


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Acta Cryst. (2013). D69, 978-990  [ doi:10.1107/S0907444913003867 ]

High-resolution powder X-ray data reveal the T6 hexameric form of bovine insulin

I. Margiolaki, A. E. Giannopoulou, J. P. Wright, L. Knight, M. Norrman, G. Schluckebier, A. N. Fitch and R. B. Von Dreele

Synopsis: High-resolution powder X-ray diffraction data have been collected to reveal the T6 hexameric insulin form and a novel approach for refining protein structures using powder diffraction data is presented.

PDB reference: 4idw

Online 11 May 2013


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Acta Cryst. (2013). D69, 991-996  [ doi:10.1107/S0907444913004046 ]

Structure and functional studies of the ribonuclease binase Glu43Ala/Phe81Ala mutant

V. A. Mitkevich, A. A. Schulga, A. A. Trofimov, P. V. Dorovatovskii, D. A. Goncharuk, E. N. Tkach, A. A. Makarov and K. M. Polyakov

Synopsis: The Glu43Ala/Phe81Ala mutation in binase prevents dimerization of the enzyme and improves its catalytic activity and cytotoxicity.

PDB reference: 4haa

Online 11 May 2013


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Acta Cryst. (2013). D69, 997-1004  [ doi:10.1107/S0907444913004745 ]

Revisiting the Haloarcula marismortui 50S ribosomal subunit model

A. Gabdulkhakov, S. Nikonov and M. Garber

Synopsis: The 2.4 Å resolution crystal structure of the H. marismortui large ribosomal subunit has been re-refined; the structures of r-proteins P0 and P1 were visualized in part and r-protein LX and helix 76 of the 23S rRNA were localized.

PDB references: 4hub and 4i4m

Online 11 May 2013


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Acta Cryst. (2013). D69, 1005-1012  [ doi:10.1107/S0907444913004034 ]

Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis

N. V. Pletneva, V. Z. Pletnev, E. Souslova, D. M. Chudakov, S. Lukyanov, V. I. Martynov, S. Arhipova, I. Artemyev, A. Wlodawer, Z. Dauter and S. Pletnev

Synopsis: The yellow fluorescent protein phiYFPv with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium.

PDB reference: 4he4

Online 11 May 2013


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Acta Cryst. (2013). D69, 1013-1025  [ doi:10.1107/S090744491300440X ]

Structure of starch synthase I from barley: insight into regulatory mechanisms of starch synthase activity

J. A. Cuesta-Seijo, M. M. Nielsen, L. Marri, H. Tanaka, S. R. Beeren and M. M. Palcic

Synopsis: The crystal structure of starch synthase I from barley was refined to 2.7 Å resolution. It includes a regulatory disulfide and a bound oligosaccharide. Activity assays were performed on several mutants.

PDB reference: 4hln

Online 14 May 2013


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Acta Cryst. (2013). D69, 1026-1037  [ doi:10.1107/S0907444913004617 ]

Structure of the Triatoma virus capsid

G. Squires, J. Pous, J. Agirre, G. S. Rozas-Dennis, M. D. Costabel, G. A. Marti, J. Navaza, S. Bressanelli, D. M. A. Guérin and F. A. Rey

Synopsis: The crystallographic structure of TrV shows specific morphological and functional features that clearly distinguish it from the type species of the Cripavirus genus, CrPV.

PDB reference: 3nap

Online 14 May 2013


 

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Acta Cryst. (2013). D69, 1038-1044  [ doi:10.1107/S0907444913004435 ]

The use of VLD (vive la difference) in the molecular-replacement approach: a pipeline

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

Synopsis: The VLD approach has been integrated into a molecular-replacement pipeline for automatic protein crystal structure solution.

Online 14 May 2013


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Acta Cryst. (2013). D69, 1045-1053  [ doi:10.1107/S0907444913004423 ]

Structures of the catalytic EAL domain of the Escherichia coli direct oxygen sensor

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

Synopsis: Structures of the EAL domain of the E. coli direct oxygen sensor show the active site in a nonproductive conformation that has implications for the regulatory mechanism.

PDB references: 4hu3 and 4hu4

Online 14 May 2013


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Acta Cryst. (2013). D69, 1054-1061  [ doi:10.1107/S0907444913004472 ]

New features of vault architecture and dynamics revealed by novel refinement using the deformable elastic network approach

A. Casañas, J. Querol-Audí, P. Guerra, J. Pous, H. Tanaka, T. Tsukihara, N. Verdaguer and I. Fita

Synopsis: Here, the re-refinement of the structure of the vault particle by incorporating the high-resolution information available for the R1-7 domains, using the deformable elastic network (DEN) approach and maintaining strict 39-fold noncrystallographic symmetry is reported.

PDB reference: 4hl8

Online 14 May 2013


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Acta Cryst. (2013). D69, 1062-1072  [ doi:10.1107/S0907444913004630 ]

Simulation of modulated protein crystal structure and diffraction data in a supercell and in superspace

J. J. Lovelace, P. D. Simone, V. Petrícek and G. E. O. Borgstahl

Synopsis: A computer simulation was created for a modulated protein structure along with structure factors in a periodic supercell and in superspace for the purpose of developing and validating software modifications that will be used to solve and refine modulated protein crystals.

Online 14 May 2013


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Acta Cryst. (2013). D69, 1073-1089  [ doi:10.1107/S0907444913004642 ]

Structure of Streptococcus agalactiae tip pilin GBS104: a model for GBS pili assembly and host interactions

V. Krishnan, P. Dwivedi, B. J. Kim, A. Samal, K. Macon, X. Ma, A. Mishra, K. S. Doran, H. Ton-That and S. V. L. Narayana

Synopsis: The crystal structure of a 75 kDa central fragment of GBS104, a tip pilin from the 2063V/R strain of Streptococcus agalactiae (group B streptococcus; GBS), is reported.

PDB references: 3tvy, 3two and 3txa

Online 15 May 2013


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Acta Cryst. (2013). D69, 1090-1098  [ doi:10.1107/S0907444913004939 ]

S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA

R. T. Byrne, F. Whelan, P. Aller, L. E. Bird, A. Dowle, C. M. C. Lobley, Y. Reddivari, J. E. Nettleship, R. J. Owens, A. A. Antson and D. G. Waterman

Synopsis: The putative methyltransferase CmoA is involved in the nucleoside modification of transfer RNA. X-ray crystallography and mass spectrometry are used to show that it contains a novel SAM derivative, S-adenosyl-S-carboxymethyl-L-homocysteine, in which the donor methyl group is replaced by a carboxymethyl group.

PDB reference: 4iwn

Online 15 May 2013


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Acta Cryst. (2013). D69, 1099-1107  [ doi:10.1107/S0907444913005726 ]

Structure of an outer surface lipoprotein BBA64 from the Lyme disease agent Borrelia burgdorferi which is critical to ensure infection after a tick bite

K. Brangulis, K. Tars, I. Petrovskis, A. Kazaks, R. Ranka and V. Baumanis

Synopsis: The X-ray crystal structure of an outer surface protein BBA64 from the Lyme disease agent B. burgdorferi which is necessary to cause the disease is reported and compared with that of the homologous protein CspA from B. burgdorferi.

PDB reference: 4aly

Online 15 May 2013


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Acta Cryst. (2013). D69, 1108-1114  [ doi:10.1107/S0907444913006021 ]

Structure of 2-haloacid dehalogenase from Pseudomonas syringae pv. tomato DC3000

Z. Hou, H. Zhang, M. Li and W. Chang

Synopsis: ps-2-HAD catalyses both L- and D- substrates, showing similar overall folding to L-HADs but completely different to the only structurally characterised DL-2-HAD enzyme.

PDB reference: 3vay

Online 15 May 2013


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Acta Cryst. (2013). D69, 1115-1123  [ doi:10.1107/S0907444913006409 ]

A novel inhibitor-binding site on the HIV-1 capsid N-terminal domain leads to improved crystallization via compound-mediated dimerization

C. T. Lemke, S. Titolo, N. Goudreau, A.-M. Faucher, S. W. Mason and P. Bonneau

Synopsis: The bound structure of a novel HIV-1 capsid-assembly inhibitor describes a unique inhibitor-binding site on the capsid N-terminal domain. Moreover, use of this inhibitor as a crystallization tool greatly improved the success rate of capsid N-terminal domain ternary cocrystallizations via compound-mediated synthetic dimerization.

PDB references: 4e91 and 4e92

Online 15 May 2013


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Acta Cryst. (2013). D69, 1124-1137  [ doi:10.1107/S0907444913006574 ]

Mapping the conformational space accessible to BACE2 using surface mutants and cocrystals with Fab fragments, Fynomers and Xaperones

D. W. Banner, B. Gsell, J. Benz, J. Bertschinger, D. Burger, S. Brack, S. Cuppuleri, M. Debulpaep, A. Gast, D. Grabulovski, M. Hennig, H. Hilpert, W. Huber, A. Kuglstatter, E. Kusznir, T. Laeremans, H. Matile, C. Miscenic, A. C. Rufer, D. Schlatter, J. Steyaert, M. Stihle, R. Thoma, M. Weber and A. Ruf

Synopsis: Surface-residue mutagenesis and cocrystallization with Fab fragments, Fynomers or Xaperones were used to obtain the first high-resolution crystal structures of BACE2. These map the conformational space accessible to this potential drug target.

PDB references: 3zkg, 3zki, 3zkm, 3zkn, 3zkq, 3zks, 3zkx, 3zl7 and 3zov

Online 15 May 2013


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Acta Cryst. (2013). D69, 1138-1149  [ doi:10.1107/S0907444913007117 ]

Structural analysis of the antibiotic-recognition mechanism of MarR proteins

Y.-M. Chang, C.K.-M. Chen, T.-P. Ko, M. W. Chang-Chien and A.H.-J. Wang

Synopsis: This study underscores the plasticity of the multidrug-binding pocket in MarR proteins and may help for the understanding of the antimicrobial resistance mechanism in pathogens.

PDB references: 4eju, 4ejv, 4ejw, 4em1, 4em2 and 4em0

Online 16 May 2013


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Acta Cryst. (2013). D69, 1150-1159  [ doi:10.1107/S0907444913007208 ]

X-ray structure of the first `extremo-[alpha]-carbonic anhydrase', a dimeric enzyme from the thermophilic bacterium Sulfurihydrogenibium yellowstonense YO3AOP1

A. Di Fiore, C. Capasso, V. De Luca, S. M. Monti, V. Carginale, C. T. Supuran, A. Scozzafava, C. Pedone, M. Rossi and G. De Simone

Synopsis: The crystal structure of SspCA, a novel `extremo-[alpha]-carbonic anhydrase', is described, providing an elucidation of the factors responsible for its function at high temperature.

PDB reference: 4g7a

Online 16 May 2013


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Acta Cryst. (2013). D69, 1160-1170  [ doi:10.1107/S0907444913004770 ]

High-resolution crystal structure of the catalytic domain of human dual-specificity phosphatase 26

E.-Y. Won, Y. Xie, C. Takemoto, L. Chen, Z.-J. Liu, B.-C. Wang, D. Lee, E.-J. Woo, S. G. Park, M. Shirouzu, S. Yokoyama, S. J. Kim and S.-W. Chi

Synopsis: This study presents crystal structures of the catalytic domain of human DUSP26 and a catalytically inactive mutant at 1.67 and 2.20 Å resolution, respectively.

PDB references: 2e0t and 4b04

Online 16 May 2013


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Acta Cryst. (2013). D69, 1171-1179  [ doi:10.1107/S0907444913007191 ]

New model-fitting and model-completion programs for automated iterative nucleic acid refinement

K. Yamashita, Y. Zhou, I. Tanaka and M. Yao

Synopsis: New programs for automated nucleic acid structure refinement, NAFIT and NABUILD, are described. They fit and extend the nucleic acid model and work with the automated iterative refinement system LAFIRE.

Online 16 May 2013


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Acta Cryst. (2013). D69, 1180-1190  [ doi:10.1107/S0907444913007798 ]

Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn2+ and Zn2+ ions

P. Drozdzal, M. Gilski, R. Kierzek, L. Lomozik and M. Jaskolski

Synopsis: Ultrahigh-resolution crystal structures of metal complexes of self-complementary Z-DNA with the sequence d(CG)3 revealed different coordination patterns for Mn2+ (octahedral) and Zn2+ (octahedral and tetrahedral) cations. The complete sperminium cation is visible in electron density in the Mn2+ structure, while in the Zn2+ structure it is partly disordered in unison with fragments of the DNA molecule.

PDB references: 4hig and 4hif

Online 16 May 2013


addenda and errata


 

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Acta Cryst. (2013). D69, 1191  [ doi:10.1107/S0907444913012158 ]

Novel c-di-GMP recognition modes of the mouse innate immune adaptor protein STING. Corrigendum

K.-H. Chin, Z.-L. Tu, Y.-C. Su, Y.-J. Yu, H.-C. Chen, Y.-C. Lo, C.-P. Chen, G. N. Barber, M.L.-C. Chuah, Z.-X. Liang and S.-H. Chou

Synopsis: The article by Chin et al. [(2013). Acta Cryst. D69, 532-366] is corrected.

PDB references: 4g3l and 4g4d

Online 17 May 2013


 

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Acta Cryst. (2013). D69, 1192  [ doi:10.1107/S0907444913003284 ]

Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis. Corrigendum

T. Koval', P. Lipovová, T. Podzimek, J. Matousek, J. Dusková, T. Skálová, A. Stepánková, J. Hasek and J. Dohnálek

Synopsis: A correction is made to the article by Koval' et al. [(2013). Acta Cryst. D69, 213-226].

Online 17 May 2013


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