Acta Crystallographica Section D

Biological Crystallography

Volume 68, Part 12 (December 2012)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Three rotamers of anti-HIV actinohivin bound to [alpha](1-2)mannobioses, which are oriented with 120° rotations around the molecular pseudo-rotation axis, are packed randomly to occupy the same positions in a unit cell according to the P212121 symmetry, so that the crystal exhibits an apparent space group P213 as a statistical structure (p. 1671). Fortunately, however, the high-resolution X-ray structure allows us to see the detailed interaction geometry of the protein with high specificity against the targets.

research papers


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Acta Cryst. (2012). D68, 1591-1603  [ doi:10.1107/S0907444912038607 ]

The structure of a thermostable mutant of pro-papain reveals its activation mechanism

S. Roy, D. Choudhury, P. Aich, J. K. Dattagupta and S. Biswas

Synopsis: Structure of the zymogen of a thermostable mutant of papain has been solved at 2.6 Å. Structural results together with biochemical studies explain the pro-peptide mediated regulation of zymogen activation.

PDB reference: 3tnx

Online 9 November 2012


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Acta Cryst. (2012). D68, 1604-1612  [ doi:10.1107/S0907444912038917 ]

Structure-activity correlations of variant forms of the B pentamer of Escherichia coli type II heat-labile enterotoxin LT-IIb with Toll-like receptor 2 binding

V. Cody, J. Pace, H. F. Nawar, N. King-Lyons, S. Liang, T. D. Connell and G. Hajishengallis

Synopsis: Structural data for the S74D variant of the pentameric B subunit of type II heat-labile enterotoxin of Escherichia coli reveal a smaller pore opening that may explain its reduced Toll-like receptor binding affinity compared to that of the wild type enterotoxin. The explanation for the enhanced Toll-like receptor binding affinity of the S74A variant is more complex than simply being attributed to the pore opening.

PDB references: 4fnf, 4fo2 and 4fp5

Online 9 November 2012


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Acta Cryst. (2012). D68, 1613-1621  [ doi:10.1107/S0907444912039042 ]

Structure of the catalytic domain of the Salmonella virulence factor SseI

S. S. Bhaskaran and C. E. Stebbins

Synopsis: The C-terminal domain of the Salmonella virulence factor SseI is structurally similar to the cysteine protease superfamily and contains the conserved catalytic triad characteristic of members of this family.

PDB references: 4g2b and 4g29

Online 9 November 2012


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Acta Cryst. (2012). D68, 1622-1631  [ doi:10.1107/S0907444912039194 ]

AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models

J. Bibby, R. M. Keegan, O. Mayans, M. D. Winn and D. J. Rigden

Synopsis: AMPLE derives successful molecular replacement search models from rapidly generated ab initio protein structure predictions.

Online 9 November 2012


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Acta Cryst. (2012). D68, 1632-1641  [ doi:10.1107/S0907444912039339 ]

Structural studies of human insulin cocrystallized with phenol or resorcinol via powder diffraction

F. Karavassili, A. E. Giannopoulou, E. Kotsiliti, L. Knight, M. Norrman, G. Schluckebier, L. Drube, A. N. Fitch, J. P. Wright and I. Margiolaki

Synopsis: The effects of the ligands phenol and resorcinol on the crystallization of human insulin have been investigated as a function of pH.

Online 9 November 2012


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Acta Cryst. (2012). D68, 1642-1652  [ doi:10.1107/S0907444912039315 ]

Substrate channels revealed in the trimeric Lactobacillus reuteri bacterial microcompartment shell protein PduB

A. Pang, M. Liang, M. B. Prentice and R. W. Pickersgill

Synopsis: The crystal structure of the trimeric shell protein PduB from L. reuteri suggests that the subunit pores act as channels for the substrate glycerol.

PDB reference: 4fay

Online 9 November 2012


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Acta Cryst. (2012). D68, 1653-1659  [ doi:10.1107/S0907444912039686 ]

Structural basis for the influence of a single mutation K145N on the oligomerization and photoswitching rate of Dronpa

N. Nguyen Bich, B. Moeyaert, K. Van Hecke, P. Dedecker, H. Mizuno, J. Hofkens and L. Van Meervelt

Synopsis: The structure of the on-state of PDM1-4, a single mutant of Dronpa, is reported, demonstrating the importance of [beta]-barrel flexibility on the photoswitching kinetics by means of oligomerization.

PDB reference: 4emq

Online 9 November 2012


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Acta Cryst. (2012). D68, 1660-1670  [ doi:10.1107/S0907444912040206 ]

X-ray study of the conformational changes in the molecule of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis during the catalyzed reaction

V. Timofeev, E. Smirnova, L. Chupova, R. Esipov and I. Kuranova

Synopsis: Based on the X-ray structures of apo PPATMt and its complexes with functionally important ligands (ATP and dPCoA) determined in the current work and in previous work, the conformational changes which accompany the reaction catalyzed by the enzyme have been studied.

PDB references: 4e1a and 3uc5

Online 9 November 2012


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Acta Cryst. (2012). D68, 1671-1679  [ doi:10.1107/S0907444912040498 ]

Structural insights into the specific anti-HIV property of actinohivin: structure of its complex with the [alpha](1-2)mannobiose moiety of gp120

M. M. Hoque, K. Suzuki, M. Tsunoda, J. Jiang, F. Zhang, A. Takahashi, N. Ohbayashi, X. Zhang, H. Tanaka, S. Omura and A. Takénaka

Synopsis: X-ray analysis of anti-HIV actinohivin in complex with the target [alpha](1-2)mannobiose moiety of high-mannose type glycans attached to HIV-1 gp120 reveals that the three rotamers generated with 120 rotations around the molecular pseudo-rotation axis are packed randomly in the unit cell according to the P212121 symmetry to exhibit an apparent space group P213 as the statistical structure. However, the high-resolution X-ray structure shows the detailed interaction geometry for specific binding.

PDB reference: 4den

Online 9 November 2012


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Acta Cryst. (2012). D68, 1680-1689  [ doi:10.1107/S0907444912041637 ]

Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio

D. Liebschner, K. Brzezinski, M. Dauter, Z. Dauter, M. Nowak, J. Kur and M. Olszewski

Synopsis: The N-terminal domain of the PriB protein from the thermophilic bacterium T. tengcongensis (TtePriB) was expressed and its crystal structure has been solved at the atomic resolution of 1.09 Å by direct methods.

PDB reference: 4gs3

Online 9 November 2012


short communications


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Acta Cryst. (2012). D68, 1690-1693  [ doi:10.1107/S0907444912039029 ]

ScrewFit: combining localization and description of protein secondary structure

P. A. Calligari and G. R. Kneller

Synopsis: An extension of the ScrewFit method is presented which combines the geometrical description of protein secondary structure in terms of local screw motions relating consecutive peptide planes with the detection of secondary-structure elements.

Online 9 November 2012


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Acta Cryst. (2012). D68, 1694-1696  [ doi:10.1107/S0907444912040176 ]

Measurement of detergent concentration using 2,6-dimethylphenol in membrane-protein crystallization

C. Prince and Z. Jia

Synopsis: Membrane proteins require detergents for their stabilization in vitro, but detergents can interfere with downstream experiments such as crystallography. This work provides an efficient way to measure the concentrations of the glycosidic detergents most commonly used in crystallography.

Online 9 November 2012


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Acta Cryst. (2012). D68, 1697-1700  [ doi:10.1107/S0907444912040590 ]

Nearest-cell: a fast and easy tool for locating crystal matches in the PDB

V. Ramraj, G. Evans, J. M. Diprose and R. M. Esnouf

Synopsis: A fast and easy tool to locate unit-cell matches in the PDB is described.

Online 9 November 2012


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