Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 10 (October 2013)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: The HOT75 D97N variant of blue-light-absorbing proteorhodopsin (p. 1965) forming pentameric rings in three-dimensional crystals composed of stacked two-dimensional crystals (type I membrane protein crystals).

scientific comment


thumbnail of article figure

[HTML version][PDF version]   [RE]  [Buy article online]

Acta Cryst. (2013). D69, 1865-1866  [ doi:10.1107/S090744491301528X ]

On the propagation of errors

M. Jaskolski

Synopsis: The policy of the Protein Data Bank that the first deposition of a small-molecule ligand, even with erroneous atom numbering, sets a precedent over accepted nomenclature rules is disputed.

Online 20 September 2013


research papers


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]   [AD]  [Buy article online]

Acta Cryst. (2013). D69, 1867-1875  [ doi:10.1107/S090744491301531X ]

Structure of the periplasmic copper-binding protein CueP from Salmonella enterica serovar Typhimurium

B.-Y. Yoon, Y.-H. Kim, N. Kim, B.-Y. Yun, J.-S. Kim, J.-H. Lee, H.-S. Cho, K. Lee and N.-C. Ha

Synopsis: In this study, the crystal structure of CueP, a periplasmic copper-binding protein from Salmonella enterica, has been determined, revealing a V-shaped dimeric structure.

PDB reference: 4gqz

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 1876-1888  [ doi:10.1107/S0907444913015771 ]

Functional convergence of structurally distinct thioesterases from cyanobacteria and plants involved in phylloquinone biosynthesis

F. Furt, W. J. Allen, J. R. Widhalm, P. Madzelan, R. C. Rizzo, G. Basset and M. A. Wilson

Synopsis: The crystal structures of two 1,4-dihydroxy-2-naphthoyl-CoA thioesterases of plant and cyanobacterial origin that are involved in the biosynthesis of phylloquinone are presented. The divergent structures of these two functionally similar enzymes indicate convergent evolution.

PDB references: 4k00 and 4k02

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2013). D69, 1889-1900  [ doi:10.1107/S090744491301576X ]

Complex structure of type VI peptidoglycan muramidase effector and a cognate immunity protein

T. Wang, J. Ding, Y. Zhang, D.-C. Wang and W. Liu

Synopsis: The structure of the Tse3-Tsi3 complex associated with the bacterial type VI secretion system of P. aeruginosa has been solved and refined at 1.9 Å resolution. The structural basis of the recognition of the muramidase effector and its inactivation by its cognate immunity protein is revealed.

PDB reference: 3wa5

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]   [AD]  [Buy article online]

Acta Cryst. (2013). D69, 1901-1910  [ doi:10.1107/S0907444913016296 ]

A quality comparison of protein crystals grown under containerless conditions generated by diamagnetic levitation, silicone oil and agarose gel

H.-L. Cao, L.-H. Sun, J. Li, L. Tang, H.-M. Lu, Y.-Z. Guo, J. He, Y.-M. Liu, X.-Z. Xie, H.-F. Shen, C.-Y. Zhang, W.-H. Guo, L.-J. Huang, P. Shang, J.-H. He and D.-C. Yin

Synopsis: The diamagnetic levitation technique can aid in obtaining high-quality protein crystals. Comparison of the results obtained using three containerless conditions indicated that the diamagnetic levitation technique exhibited the greatest improvement in crystal quality, followed by that using agarose gel.

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 1911-1920  [ doi:10.1107/S0907444913016600 ]

Structure of the JmjC-domain-containing protein JMJD5

H. Wang, X. Zhou, M. Wu, C. Wang, X. Zhang, Y. Tao, N. Chen and J. Zang

Synopsis: The crystal structure of JMJD5176-C revealed that three residues with large side chains located at the entrance to the substrate-binding pocket abolish the histone demethylase activity of this fragment of JMJD5. The structural similarity of JMJD5 to FIH suggested that human JMJD5 might function as a protein hydroxylase.

PDB reference: 4gaz

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 1921-1934  [ doi:10.1107/S0907444913016673 ]

On effective and optical resolutions of diffraction data sets

L. Urzhumtseva, B. Klaholz and A. Urzhumtsev

Synopsis: The notion of `resolution' is discussed and a formal definition applicable to various diffraction data sets, both complete and incomplete and both isotropic and anisotropic, is suggested.

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2013). D69, 1935-1945  [ doi:10.1107/S0907444913016776 ]

Structural basis for the antibody neutralization of Herpes simplex virus

C.-C. Lee, L.-L. Lin, W.-E. Chan, T.-P. Ko, J.-S. Lai and A.H.-J. Wang

Synopsis: The gD-E317-Fab complex crystal revealed the conformational epitope of human mAb E317 on HSV gD, providing a molecular basis for understanding the viral neutralization mechanism.

PDB references: 3w9d and 3w9e

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 1946-1957  [ doi:10.1107/S0907444913017642 ]

A functional and structural study of the major metalloprotease secreted by the pathogenic fungus Aspergillus fumigatus

D. Fernández, S. Russi, J. Vendrell, M. Monod and I. Pallarès

Synopsis: The secreted success of cone-moulded weapons: unveiling the structural and functional details of the major collagenolytic and elastinolytic zinc-dependent proteinase from Aspergillus fumigatus.

PDB reference: 4k90

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 1958-1964  [ doi:10.1107/S0907444913018003 ]

Structure of the polypeptide crotamine from the Brazilian rattlesnake Crotalus durissus terrificus

M. A. Coronado, A. Gabdulkhakov, D. Georgieva, B. Sankaran, M. T. Murakami, R. K. Arni and C. Betzel

Synopsis: The crystal structure of the antitumoral and cell-penetrating polypeptide crotamine from C. durissus terrificus venom is reported.

PDB reference: 4gv5

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 1965-1980  [ doi:10.1107/S0907444913017575 ]

Cross-protomer interaction with the photoactive site in oligomeric proteorhodopsin complexes

T. Ran, G. Ozorowski, Y. Gao, O. A. Sineshchekov, W. Wang, J. L. Spudich and H. Luecke

Synopsis: The first crystal structure of a proteorhodopsin shows a hexametric ring of protein in which the conserved photoactive-site histidine forms a hydrogen bond to the Schiff base proton acceptor from the same molecule and also to a tryptophan residue of a neighboring protomer. The structure and mutant studies reveal novel aspects of the ion translocation mechanism and cooperative behavior between protomers involving the inter-molecular His-Trp pair.

PDB references: 4jq6, 4kly and 4knf

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2013). D69, 1981-1994  [ doi:10.1107/S0907444913017800 ]

Rv2969c, essential for optimal growth in Mycobacterium tuberculosis, is a DsbA-like enzyme that interacts with VKOR-derived peptides and has atypical features of DsbA-like disulfide oxidases

L. Premkumar, B. Heras, W. Duprez, P. Walden, M. Halili, F. Kurth, D. P. Fairlie and J. L. Martin

Synopsis: The gene product of M. tuberculosis Rv2969c is shown to be a disulfide oxidase enzyme that has a canonical DsbA-like fold with novel structural and functional characteristics.

PDB reference: 4k6x

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 1995-2007  [ doi:10.1107/S0907444913017320 ]

The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators

A. M. Alanazi, E. L. Neidle and C. Momany

Synopsis: The first structures of DNA-protein complexes that include the DNA-binding domain from a LysR-type transcriptional regulator (LTTR) are described here and are used to explain the high degree of conservation in a DNA-sequence motif recognized by LTTRs (T-N11-A). Sequence-specific recognition depends primarily on direct protein-nucleotide base contacts.

PDB references: 3m1e, 4ihs and 4iht

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2008-2016  [ doi:10.1107/S0907444913017046 ]

High-resolution structure of an atypical [alpha]-phosphoglucomutase related to eukaryotic phosphomannomutases

P. Nogly, P. M. Matias, M. de Rosa, R. Castro, H. Santos, A. R. Neves and M. Archer

Synopsis: The structure of [alpha]-phosphoglucomutase from L. lactis reveals overall structure similarity to eukaryotic phosphomannomutases, but with differences at the active site.

PDB reference: 4bnd

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2017-2026  [ doi:10.1107/S0907444913018015 ]

High-resolution structure of a papaya plant-defence barwin-like protein solved by in-house sulfur-SAD phasing

J. Huet, E. J. Teinkela Mbosso, S. Soror, F. Meyer, Y. Looze, R. Wintjens and A. Wohlkönig

Synopsis: The first crystal structure of a barwin-like protein is determined at high resolution by single-wavelength anomalous diffraction phasing using the six intrinsic sulfur atoms present in the protein.

PDB references: 4jp6 and 4jp7

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2027-2038  [ doi:10.1107/S090744491301799X ]

The structure of a glycoside hydrolase family 81 endo-[beta]-1,3-glucanase

P. Zhou, Z. Chen, Q. Yan, S. Yang, R. Hilgenfeld and Z. Jiang

Synopsis: The crystal structure of the endo-[beta]-1,3-glucanase from Rhizomucor miehei (RmLam81A) was determined in two crystal forms at 2.3 and 2.0 Å resolution, respectively. The structure of RmLam81A is greatly different from all endo-[beta]-1,3-glucanase structures available.

PDB references: 4k3a and 4k35

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version]  [Open access]

Acta Cryst. (2013). D69, 2039-2049  [ doi:10.1107/S0907444913018167 ]

Improving experimental phases for strong reflections prior to density modification

M. Uervirojnangkoorn, R. Hilgenfeld, T. C. Terwilliger and R. J. Read

Synopsis: A genetic algorithm has been developed to optimize the phases of the strongest reflections in SIR/SAD data. This is shown to facilitate density modification and model building in several test cases.

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2050-2060  [ doi:10.1107/S0907444913018714 ]

Structural characterization of gephyrin by AFM and SAXS reveals a mixture of compact and extended states

B. Sander, G. Tria, A. V. Shkumatov, E.-Y. Kim, J. G. Grossmann, I. Tessmer, D. I. Svergun and H. Schindelin

Synopsis: A combination of small-angle X-ray scattering and atomic force microscopy reveals that the trimeric two-domain protein gephyrin adopts a multitude of compact and extended conformations, with a preference for compact states. This behaviour is caused by the long and primarily unstructured linker region, which also interacts with the structured domains located at either end of gephyrin. Potential functional implications of the structural data are discussed.

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 2061-2071  [ doi:10.1107/S0907444913019197 ]

Structure of fully liganded Hb [zeta]2[beta]2s trapped in a tense conformation

M. K. Safo, T.-P. Ko, O. Abdulmalik, Z. He, A.H.-J. Wang, E. R. Schreiter and J. E. Russell

Synopsis: The crystallographic analysis of fully liganded Hb [zeta]2[beta]2s trapped in a tense conformation is reported.

PDB reference: 3w4u

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2072-2080  [ doi:10.1107/S0907444913019276 ]

Determination of the GH3.12 protein conformation through HPLC-integrated SAXS measurements combined with X-ray crystallography

A. Round, E. Brown, R. Marcellin, U. Kapp, C. S. Westfall, J. M. Jez and C. Zubieta

Synopsis: Combined small-angle X-ray scattering (SAXS) and crystallographic data were used to probe the two-step catalytic mechanism of the acyl acid-amido synthetase GH3.12. On-line size-exclusion chromatography directly upstream of the X-ray beam improved the sample homogeneity and allowed the determination of changes in the protein conformation in solution. X-ray models were fitted to the SAXS data to unambiguously determine the protein conformation in the presence of different ligands.

PDB reference: 4l39

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 2081-2090  [ doi:10.1107/S0907444913019379 ]

Structure of the Sgt2 dimerization domain complexed with the Get5 UBL domain involved in the targeting of tail-anchored membrane proteins to the endoplasmic reticulum

J.-Y. Tung, Y.-C. Li, T.-W. Lin and C.-D. Hsiao

Synopsis: The structure of the complex between the N-terminal dimerization domain of Sgt2 and the ubiquitin-like domain of Get5 was determined in order to understand the interaction between Sgt2 and Get5 and to reveal how this complex is essential for the function of TA-protein delivery under stress conditions.

PDB reference: 3zdm

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2091-2103  [ doi:10.1107/S0907444913019471 ]

Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis

D. V. Svintradze, D. L. Peterson, E. A. Collazo-Santiago, J. P. Lewis and H. T. Wright

Synopsis: Differences in OxyR regulated expression of oxidative stress genes between Escherichia coli and Porphyromonas gingivalis are explained by very minor differences in structure and amino-acid sequence of the respective oxidized and reduced OxyR regulatory domains. These differences affect OxyR quaternary structures and are predicted from model building of full length OxyR-DNA complexes to confer distinct modes of DNA binding on this transcriptional regulator.

PDB references: 3ho7, 3t22 and 3uki

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 2104-2115  [ doi:10.1107/S0907444913020349 ]

Structure of a bifunctional alcohol dehydrogenase involved in bioethanol generation in Geobacillus thermoglucosidasius

J. Extance, S. J. Crennell, K. Eley, R. Cripps, D. W. Hough and M. J. Danson

Synopsis: The crystal structure of the alcohol dehydrogenase (ADH) domain of an ADHE protein from G. thermoglucosidasius has been determined to 2.5 Å resolution. Docking of this with a homology model of the aldehyde dehydrogenase domain, for which no structure has been determined, has enabled the construction of a model of the complete ADHE and a putative mechanism of formation of the large multimeric `spirosomes' that have been reported for ADHE from this and other organisms.

PDB reference: 3zdr

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 2116-2123  [ doi:10.1107/S0907444913020507 ]

Three-dimensional domain swapping and supramolecular protein assembly: insights from the X-ray structure of a dimeric swapped variant of human pancreatic RNase

A. Pica, A. Merlino, A. K. Buell, T. P. J. Knowles, E. Pizzo, G. D'Alessio, F. Sica and L. Mazzarella

Synopsis: The intriguing crystal organization of the domain-swapped dimer of a human pancreatic ribonuclease variant indicates that the protein can form fibrils in solution. They were observed and characterized by atomic force microscopy. The importance of domain swapping in inducing native-like fibril formation is highlighted.

PDB reference: 4kxh

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2124-2135  [ doi:10.1107/S0907444913020568 ]

Structural analysis and insights into the glycon specificity of the rice GH1 Os7BGlu26 [beta]-D-mannosidase

A. Tankrathok, J. Iglesias-Fernández, S. Luang, R. C. Robinson, A. Kimura, C. Rovira, M. Hrmova and J. R. Ketudat Cairns

Synopsis: The structures of rice Os7BGlu26 [beta]-D-mannosidase, of its product complex with [beta]-D-mannose and of Os7BGlu26 computationally docked with 4-nitrophenyl [beta]-D-mannoside suggest that the D-mannose pyranose ring makes a conformational transition from OS2 skew boat to B2,5 boat to 1S5 skew boat during the deglycosylation of the enzyme in hydrolysis. These structures led to the hypothesis that the residues interacting with the catalytic acid/base play a role in determining [beta]-D-mannosidase activity, which was supported by site-directed mutagenesis and kinetic analysis.

PDB references: 4jho and 4jie

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2136-2145  [ doi:10.1107/S0907444913020556 ]

Conformational changes in human prolyl-tRNA synthetase upon binding of the substrates proline and ATP and the inhibitor halofuginone

J. Son, E. H. Lee, M. Park, J. H. Kim, J. Kim, S. Kim, Y. H. Jeon and K. Y. Hwang

Synopsis: Three crystal structures of the prolyl-tRNA synthetase domain of human glutamyl-prolyl-tRNA synthetase, two of which were complexed with small molecules, were determined by Zn-SAD phasing combined with molecular replacement. The structures revealed that conformational changes occur in the active site upon small-molecule binding.

PDB references: 4k86, 4k87 and 4k88

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 2146-2156  [ doi:10.1107/S0907444913020830 ]

Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue

B. D. Wallentine, Y. Wang, V. Tretyachenko-Ladokhina, M. Tan, D. F. Senear and H. Luecke

Synopsis: X-ray crystallographic structures of four p53 core-domain variants were determined in order to gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53.

PDB references: 4kvp, 4lo9, 4loe and 4lof

Online 20 September 2013


short communications


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 2157-2160  [ doi:10.1107/S0907444913019604 ]

The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography

F. Meilleur, P. Munshi, L. Robertson, A. D. Stoica, L. Crow, A. Kovalevsky, T. Koritsanszky, B. C. Chakoumakos, R. Blessing and D. A. A. Myles

Synopsis: The first neutron protein structure refined against 1.75 Å resolution data collected on the new IMAGINE instrument at HFIR (ORNL) is reported.

PDB reference: 4k9f

Online 20 September 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 2161-2164  [ doi:10.1107/S090744491301994X ]

Different orientations of low-molecular-weight fragments in the binding pocket of a BRD4 bromodomain

G. Lolli and R. Battistutta

Synopsis: Different orientations of similar low-molecular-weight fragments in the acetylated lysine-recognition pocket of the BRD4 N-terminal bromodomain are reported.

PDB references: 4ioo, 4ioq and 4ior

Online 20 September 2013


Copyright © International Union of Crystallography
IUCr Webmaster