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December 2012 issue
Cover illustration: Three rotamers of anti-HIV actinohivin bound to ![[alpha]](/logos/entities/alpha_rmgif.gif)
(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 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
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: thermostable mutant of pro-papain, 3tnx
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.
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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.
AMPLE derives successful molecular replacement search models from rapidly generated ab initio protein structure predictions.
The effects of the ligands phenol and resorcinol on the crystallization of human insulin have been investigated as a function of pH.
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: PduB, 4fay
The structure of the on-state of PDM1-4, a single mutant of Dronpa, is reported, demonstrating the importance of β-barrel flexibility on the photoswitching kinetics by means of oligomerization.
PDB reference: PDM1-4, 4emq
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.
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X-ray analysis of anti-HIV actinohivin in complex with the target α(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: actinohivin in complex with MB, 4den
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: N-terminal domain of PriB, 4gs3
short communications
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.
Measurement of detergent concentration using 2,6-dimethylphenol in membrane-protein crystallization
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.
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A fast and easy tool to locate unit-cell matches in the PDB is described.
