Acta Crystallographica Section D

Biological Crystallography

Volume 70, Part 1 (January 2014)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: An E177Q variant of the family 11 xylanase secreted by the filamentous fungus Trichoderma reesei complexed with xylohexaose (p. 11).

letters to the editor


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Acta Cryst. (2014). D70, 1  [ doi:10.1107/S1399004713024905 ]

Doing the right things

M. Jaskolski

Synopsis: Recent examples of the misrepresentation of biological helical structures in the popular media are identified and discussed.

Online 24 December 2013


research papers


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Acta Cryst. (2014). D70, 2-10  [ doi:10.1107/S139900471302333X ]

Structure of the TRAF4 TRAF domain with a coiled-­coil domain and its implications for the TRAF4 signalling pathway

J. H. Yoon, Y. Cho and H. H. Park

Synopsis: TRAF4 is a unique family of TRAF, which participates in many ontogenic processes. The crystal structure of TRAF domain of TRAF4 was solved at 2.3 Å resolution.

PDB reference: 4k8u

Online 24 December 2013


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Acta Cryst. (2014). D70, 11-23  [ doi:10.1107/S1399004713023626 ]

X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism

Q. Wan, Q. Zhang, S. Hamilton-Brehm, K. Weiss, M. Mustyakimov, L. Coates, P. Langan, D. Graham and A. Kovalevsky

Synopsis: X-ray structures of a family 11 xylanase with bound xylohexaose substrate or products revealed six sugar-binding subsites in the active site of the enzyme. Replacing amino acids near the catalytic glutamic acid 177 decreased the xylanase activity but increased the relative activity at alkaline pH.

PDB references: 4hk8, 4hk9, 4hkl, 4hkw and 4hko

Online 24 December 2013


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Acta Cryst. (2014). D70, 24-30  [ doi:10.1107/S1399004713024437 ]

Crystallographic snapshots of initial steps in the collapse of the calmodulin central helix

P. Kursula

Synopsis: Novel bent conformations of the calmodulin central helix are presented. The structures may relate to the initial stages of structural collapse in calmodulin upon target-peptide binding.

PDB references: 4bw7 and 4bw8

Online 24 December 2013


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Acta Cryst. (2014). D70, 31-39  [ doi:10.1107/S1399004713024644 ]

The rotational order-disorder structure of the reversibly photoswitchable red fluorescent protein rsTagRFP

S. Pletnev, F. V. Subach, V. V. Verkhusha and Z. Dauter

Synopsis: An analysis of the rotational order-disorder structure of the reversibly photoswitchable red fluorescent protein rsTagRFP is presented.

PDB reference: 4kpi

Online 24 December 2013


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Acta Cryst. (2014). D70, 40-47  [ doi:10.1107/S1399004713024619 ]

Structure and mechanism of a type III secretion protease, NleC

W. Li, Y. Liu, X. Sheng, P. Yin, F. Hu, Y. Liu, C. Chen, Q. Li, C. Yan and J. Wang

Synopsis: The crystal structure of NleC is reported at 1.55 Å resolution. In conjunction with biochemical analyses, the structure reveals that NleC is a member of the zincin zinc protease family and that the configuration of the NleC active site resembles that of the metzincin clan of metallopeptidases.

PDB references: 4lgi and 4lgj

Online 24 December 2013


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Acta Cryst. (2014). D70, 48-57  [ doi:10.1107/S139900471302364X ]

Lysine carboxylation: unveiling a spontaneous post-translational modification

D. Jimenez-Morales, L. Adamian, D. Shi and J. Liang

Synopsis: A computational method for the prediction of lysine carboxylation (KCX) in protein structures is described. The method accurately identifies misreported KCXs and predicts previously unknown KCX sites.

Online 24 December 2013


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Acta Cryst. (2014). D70, 58-67  [ doi:10.1107/S1399004713024218 ]

The regulatory mechanism of the caspase 6 pro-domain revealed by crystal structure and biochemical assays

Q. Cao, X.-J. Wang, L.-F. Li and X.-D. Su

Synopsis: The regulatory mechanism of the caspase 6 pro-domain is revealed.

PDB reference: 4iyr

Online 24 December 2013


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Acta Cryst. (2014). D70, 68-78  [ doi:10.1107/S1399004713025030 ]

Structural characterization of new deoxycytidine kinase inhibitors rationalizes the affinity-determining moieties of the molecules

J. Nomme, J. M. Murphy, Y. Su, N. D. Sansone, A. L. Armijo, S. T. Olson, C. Radu and A. Lavie

Synopsis: This article describes the structural and biochemical characterization of a new class of high-affinity and selective human deoxycytidine kinase inhibitors.

PDB references: 4jlj, 4jlk, 4jlm and 4jln

Online 24 December 2013


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Acta Cryst. (2014). D70, 79-90  [ doi:10.1107/S1399004713024838 ]

Structural basis for the broad specificity of a new family of amino-acid racemases

A. Espaillat, C. Carrasco-López, N. Bernardo-García, N. Pietrosemoli, L. H. Otero, L. Álvarez, M. A. de Pedro, F. Pazos, B. M. Davis, M. K. Waldor, J. A. Hermoso and F. Cava

Synopsis: This work reports the crystal structure of BsrV, the broad spectrum racemase of Vibrio cholerae (1.15 Å resolution); unveils signature amino acids associated to its multispecificity and uses this signature sequence to identify a large family of BsrV-like multi-specific racemases in bacteria. Structural analyses of an additional Bsr confirmed the distinguishing features are conserved among Bsr-family members.

PDB references: 4beu, 4beq, 4bf5 and 4bhy

Online 24 December 2013


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Acta Cryst. (2014). D70, 91-100  [ doi:10.1107/S1399004713025285 ]

Atomic resolution crystal structure of glutaredoxin 1 from Plasmodium falciparum and comparison with other glutaredoxins

M. Yogavel, T. Tripathi, A. Gupta, M. M. Banday, S. Rahlfs, K. Becker, H. Belrhali and A. Sharma

Synopsis: The structure of glutaredoxin 1 from P. falciparum has been determined at atomic resolution and its unique structural features have been dissected.

PDB references: 4hjm, 4kje and 4kjf

Online 24 December 2013


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Acta Cryst. (2014). D70, 101-109  [ doi:10.1107/S1399004713025431 ]

Breaking the indexing ambiguity in serial crystallography

W. Brehm and K. Diederichs

Synopsis: In serial crystallography, it is demonstrated that the indexing mode of partial data sets can be established using correlation coefficients against other data sets and a clustering procedure. For 24 chiral space groups clustering can be performed in two dimensions, but in space groups P3, P31 and P32 clustering in three or four dimensions is required.

Online 24 December 2013


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Acta Cryst. (2014). D70, 110-122  [ doi:10.1107/S1399004713029040 ]

Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T6 bovine insulin derivatives

C. G. Frankaer, S. Mossin, K. Ståhl and P. Harris

Synopsis: The level of structural detail around the metal sites in Ni2+ and Cu2+ T6 insulin derivatives was significantly improved by using a combination of single-crystal X-ray crystallography and X-ray absorption spectroscopy. Photoreduction and subsequent radiation damage of the Cu2+ sites in Cu insulin was followed by XANES spectroscopy.

PDB references: 4m4f, 4m4h, 4m4i, 4m4j, 4m4l and 4m4m

Online 24 December 2013


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Acta Cryst. (2014). D70, 123-133  [ doi:10.1107/S1399004713028721 ]

The crystal structure and biochemical characterization of Kif15: a bifunctional molecular motor involved in bipolar spindle formation and neuronal development

M. Klejnot, A. Falnikar, V. Ulaganathan, R. A. Cross, P. W. Baas and F. Kozielski

Synopsis: The structural and biochemical study of Kif15 provides insight into this potential drug target and allows comparison with Eg5, a kinesin that partially shares the functions of Kif15.

PDB reference: 4bn2

Online 24 December 2013


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Acta Cryst. (2014). D70, 134-143  [ doi:10.1107/S1399004713030071 ]

Ligand placement based on prior structures: the guided ligand-replacement method

H. E. Klei, N. W. Moriarty, N. Echols, T. C. Terwilliger, E. T. Baldwin, M. Pokross, S. Posy and P. D. Adams

Synopsis: A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available.

Online 25 December 2013


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Acta Cryst. (2014). D70, 144-154  [ doi:10.1107/S139900471302748X ]

Automating crystallographic structure solution and refinement of protein-ligand complexes

N. Echols, N. W. Moriarty, H. E. Klei, P. V. Afonine, G. Bunkóczi, J. J. Headd, A. J. McCoy, R. D. Oeffner, R. J. Read, T. C. Terwilliger and P. D. Adams

Synopsis: A software system for automated protein-ligand crystallography has been implemented in the Phenix suite. This significantly reduces the manual effort required in high-throughput crystallographic studies.

Online 25 December 2013


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Acta Cryst. (2014). D70, 155-164  [ doi:10.1107/S1399004713025820 ]

Structure of the FP domain of Fbxo7 reveals a novel mode of protein-protein interaction

J. Shang, G. Wang, Y. Yang, X. Huang and Z. Du

Synopsis: The FP domain of the human F-box protein Fbxo7 adopts an [alpha]/[beta]-fold structure that is similar to the FP domain of the human proteasome inhibitor PI31. However, the two FP domains show dramatic differences in the way that they mediate protein-protein interactions.

PDB references: 4l9c and 4l9h

Online 31 December 2013


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Acta Cryst. (2014). D70, 165-176  [ doi:10.1107/S1399004713027910 ]

Atomic resolution view into the structure-function relationships of the human myelin peripheral membrane protein P2

S. Ruskamo, R. P. Yadav, S. Sharma, M. Lehtimäki, S. Laulumaa, S. Aggarwal, M. Simons, J. Bürck, A. S. Ulrich, A. H. Juffer, I. Kursula and P. Kursula

Synopsis: The structure of the human myelin peripheral membrane protein P2 has been refined at 0.93 Å resolution. In combination with functional experiments in vitro, in vivo and in silico, the fine details of the structure-function relationships in P2 are emerging.

PDB reference: 4bvm

Online 31 December 2013


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Acta Cryst. (2014). D70, 177-185  [ doi:10.1107/S1399004713026655 ]

Structural enzymology of Helicobacter pylori methylthioadenosine nucleosidase in the futalosine pathway

R. Q. Kim, W. A. Offen, G. J. Davies and K. A. Stubbs

Synopsis: Crystal structures of the H. pylori methylthioadenosine nucleosidase (MTAN) HpyMqnB have been solved in native and complexed forms, shedding light on substrate binding and the reaction mechanism.

PDB references: 4bmx, 4bn0, 4bmz and 4bmy

Online 31 December 2013


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Acta Cryst. (2014). D70, 186-195  [ doi:10.1107/S1399004713029155 ]

Three-dimensional structure of a Streptomyces sviceus GNAT acetyltransferase with similarity to the C-terminal domain of the human GH84 O-GlcNAcase

Y. He, C. Roth, J. P. Turkenburg and G. J. Davies

Synopsis: The crystal structure of a bacterial acetyltransferase with 27% sequence identity to the C-terminal domain of human O-GlcNAcase has been solved at 1.5 Å resolution. This S. sviceus protein is compared with known GCN5-related acetyltransferases, adding to the diversity observed in this superfamily.

PDB reference: 4bmh

Online 31 December 2013


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Acta Cryst. (2014). D70, 196-202  [ doi:10.1107/S1399004713026333 ]

A novel mode of ferric ion coordination by the periplasmic ferric ion-binding subunit FbpA of an ABC-type iron transporter from Thermus thermophilus HB8

S. Wang, M. Ogata, S. Horita, J. Ohtsuka, K. Nagata and M. Tanokura

Synopsis: Crystal structures of FbpA from T. thermophilus (TtFbpA) in its apo and ferric ion-bound forms have been solved. TtFbpA shows the novel formation of a six-coordinated complex of ferric ion coordinated by three tyrosine residues, two monodentate bicarbonates and a water molecule.

PDB references: 3wae and 3waf

Online 31 December 2013


short communications


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Acta Cryst. (2014). D70, 203-208  [ doi:10.1107/S139900471302422X ]

A challenging interpretation of a hexagonally layered protein structure

M. C. Thompson and T. O. Yeates

Synopsis: The authors describe the structure determination of a hexagonally layered protein structure that suffered from a complicated combination of translational non-crystallographic symmetry and hemihedral twinning. This case serves as a reminder that broken crystallographic symmetry resulting from doubling of a unit-cell axis often requires a new choice of origin.

PDB reference: 4liw

Online 24 December 2013


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