Biological Crystallography

 

Acta Cryst. (2005). D61, 207-217  [ doi:10.1107/S0907444904030926 ]

Structural consequences of hen egg-white lysozyme orthorhombic crystal growth in a high magnetic field: validation of X-ray diffraction intensity, conformational energy searching and quantitative analysis of B factors and mosaicity

S. Saijo, Y. Yamada, T. Sato, N. Tanaka, T. Matsui, G. Sazaki, K. Nakajima and Y. Matsuura

Synopsis: It has been shown that a high magnetic field of 10  T improves the quality of lysozyme crystals as quantified by comparison of the X-ray diffraction of crystals grown in the presence and absence of a magnetic field of 10  T, from structure comparisons and from molecular-modelling studies with conformational energy searching, from analysis of the anisotropic B factors and finally from analysis of the mosaicity. It is concluded that magnetic enhancement in protein crystal perfection is an important material engineering tool in the study of protein structure and function.

PDB references: 1wtm and 1wtn

Online 24 February 2005

 

Acta Cryst. (2005). D61, 218-229  [ doi:10.1107/S0907444904031531 ]

Urate oxidase from Aspergillus flavus: new crystal-packing contacts in relation to the content of the active site

P. Retailleau, N. Colloc'h, D. Vivarès, F. Bonneté, B. Castro, M. El Hajji and T. Prangé

Synopsis: Four crystal forms of urate oxidase are found to arise from the presence or absence of flat cyclic inhibitors.

PDB references: 1ws3, 1ws2, 1wrr, 1xxj, 1xy3 and 1xt4

Online 24 February 2005

 

Acta Cryst. (2005). D61, 230-235  [ doi:10.1107/S0907444904032147 ]

Structure of Escherichia coli glutamate decarboxylase (GAD) in complex with glutarate at 2.05  Å resolution

D. I. Dutyshev, E. L. Darii, N. P. Fomenkova, I. V. Pechik, K. M. Polyakov, S. V. Nikonov, N. S. Andreeva and B. S. Sukhareva

Synopsis: The structure of the complex of E. coli glutamate decarboxylase (GAD) with the substrate analogue glutarate has been solved at 2.05  Å resolution.

PDB reference: 1xey

Online 24 February 2005

 

Acta Cryst. (2005). D61, 236-246  [ doi:10.1107/S0907444904032378 ]

Structures of the DNA-binding site of Runt-domain transcription regulators

M. Kitayner, H. Rozenberg, D. Rabinovich and Z. Shakked

Synopsis: Runt-domain (RD) proteins regulate transcription of target genes. The DNA duplex TCTGCGGTC/TGACCGCAG, incorporating the binding site for the RD transcription factors (bold), was crystallized in space group P4₃. X-ray analysis of two crystals diffracting to 1.7 and 2.0  Å resolution, which had slight variations in their unit-cell parameters, revealed two distinct conformations of the A-DNA helix.

PDB references: 1xjx and 1xjy

Online 24 February 2005

 

Acta Cryst. (2005). D61, 247-255  [ doi:10.1107/S090744490403269X ]

Strongly correlated structure of axial-symmetric proteins. I. Orthorhombic, tetragonal, trigonal and hexagonal symmetries

A. Janner

Synopsis: The architectural elements of axial-symmetric proteins, such as envelopes and channels, are characterized by lattices with a single lattice parameter and by crystallographic scale rotations.

Online 24 February 2005

 

Acta Cryst. (2005). D61, 256-268  [ doi:10.1107/S0907444904032706 ]

Strongly correlated structure of axial-symmetric proteins. II. Pentagonal, heptagonal, octagonal, nonagonal and ondecagonal symmetries

A. Janner

Synopsis: The architectural elements of axial-symmetric proteins, such as envelopes and channels, are characterized by polygonal lattices with a single lattice parameter and by crystallographic scale rotations.

Online 24 February 2005

 

Acta Cryst. (2005). D61, 269-277  [ doi:10.1107/S0907444904032718 ]

Strongly correlated structure of axial-symmetric proteins. III. Complexes with DNA/RNA

A. Janner

Synopsis: The interplay between structural elements in axial-symmetric protein-DNA (or protein-RNA) complexes is shown to be compatible with a crystallographic characterization in terms of integral polygonal lattices and scale-rotational point-group transformations.

Online 24 February 2005

 

Acta Cryst. (2005). D61, 278-284  [ doi:10.1107/S0907444904032937 ]

Structure of human uridine-cytidine kinase 2 determined by SIRAS using a rotating-anode X-ray generator and a single samarium derivative

T. C. Appleby, G. Larson, I. W. Cheney, H. Walker, J. Z. Wu, W. Zhong, Z. Hong and N. Yao

Synopsis: The crystal structure of UCK2 was determined utilizing an in-house X-ray source and a single samarium derivative.

PDB reference: 1xrj

Online 24 February 2005

 

Acta Cryst. (2005). D61, 285-293  [ doi:10.1107/S0907444904033037 ]

Phased translation function revisited: structure solution of the cofilin-homology domain from yeast actin-binding protein 1 using six-dimensional searches

B. V. Strokopytov, A. Fedorov, N. M. Mahoney, M. Kessels, D. G. Drubin and S. C. Almo

Synopsis: A modified molecular-replacement method is described that makes use of six-dimensional searches and the phased translation function, providing a systematic examination of all possible search-model orientations in an experimental electron-density map.

PDB reference: 1hqz

Online 24 February 2005

 

Acta Cryst. (2005). D61, 294-301  [ doi:10.1107/S0907444904032950 ]

Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16  Å resolution

M. Yao, Y. Yasutake, H. Morita and I. Tanaka

Synopsis: The structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii was solved by the MAD method and was refined to 2.16  Å resolution.

PDB reference: 1wls

Online 24 February 2005

 

Acta Cryst. (2005). D61, 302-308  [ doi:10.1107/S0907444904033165 ]

Structure of the zinc-induced heterodimer of two calcium-free isoforms of phospholipase A₂ from Naja naja sagittifera at 2.7  Å resolution

T. Jabeen, S. Sharma, N. Singh, R. K. Singh, A. K. Verma, M. Paramasivam, A. Srinivasan and T. P. Singh

Synopsis: The crystal structure of the zinc-induced heterodimer of two closely related isoforms of phospholipase A₂ (PLA₂) from cobra venom has been determined and refined at 2.7  Å resolution. The structure reveals that zinc ion is unable to bind in the so-called calcium-binding loop of PLA₂ and that by inducing dimerization zinc ion inactivates the two isoforms.

PDB reference: 1xxw

Online 24 February 2005

 

Acta Cryst. (2005). D61, 309-315  [ doi:10.1107/S0907444904033190 ]

The 1.70  Å X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase

P. Müller, M. R. Sawaya, I. Pashkov, S. Chan, C. Nguyen, Y. Wu, L. J. Perry and D. Eisenberg

Synopsis: The crystal structure of the cofactor-dependent phosphoglycerate mutase of M. tuberculosis has been determined at a resolution of 1.70  Å.

PDB reference: 1rii

Online 24 February 2005

 

Acta Cryst. (2005). D61, 316-321  [ doi:10.1107/S0907444904033189 ]

Structure of recombinant human cyclophilin J, a novel member of the cyclophilin family

L.-L. Huang, X.-M. Zhao, C.-Q. Huang, L. Yu and Z.-X. Xia

Synopsis: The X-ray structure of recombinant human cyclophilin J, a novel member of the cyclophilin family, has been determined at 2.6  Å resolution. The structure is similar to the cyclophilin A structure and appears to support the solvent-assisted mechanism.

PDB reference: 1xyh

Online 24 February 2005

 

Acta Cryst. (2005). D61, 322-332  [ doi:10.1107/S0907444904033669 ]

Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics

N. Yu, H. P. Yennawar and K. M. Merz

Synopsis: Energy restraints derived from linear-scaling semiempirical quantum-mechanical calculations and X-ray diffraction data are combined to refine the crystal structure of a protein molecule, bovine pancreatic trypsin inhibitor.

Online 24 February 2005

 

Acta Cryst. (2005). D61, 333-339  [ doi:10.1107/S0907444904034316 ]

X-ray crystallographic studies of two transthyretin variants: further insights into amyloidogenesis

R. M. Neto-Silva, S. Macedo-Ribeiro, P. J. B. Pereira, M. Coll, M. J. Saraiva and A. M. Damas

Synopsis: The crystal structures of two transthyretin variants TTR Y78F, an amyloidogenic protein, and TTR R104H, a non-pathogenic/protective variant, have been determined. The structural features responsible for TTR stabilization/destabilization are discussed.

PDB references: 1x7t and 1x7s

Online 24 February 2005

 

Acta Cryst. (2005). D61, 340-343  [ doi:10.1107/S0907444904033906 ]

A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba₃ oxidase from Thermus thermophilus

L. M. Hunsicker-Wang, R. L. Pacoma, Y. Chen, J. A. Fee and C. D. Stout

Synopsis: A cryoprotection scheme was developed that results in glycerol binding within the interior of the membrane-spanning domain. The His-tagged recombinant protein adopts different lattice contacts but diffracts as well as the native protein.

PDB reference: 1xme

Online 24 February 2005

 

Acta Cryst. (2005). D61, 344-349  [ doi:10.1107/S090744490403416X ]

The use of high halide-ion concentrations and automated phasing procedures for the structural analysis of BclA, the major component of the exosporium of Bacillus anthracis spores

S. Salamitou, S. Réty, F. Le Hégarat, G. Leblon and A. Lewit-Bentley

Synopsis: The structure determination of the major outer surface antigen of the B. anthracis spore using automated phasing programs and exploiting the anomalous signal from iodide is presented.

Online 24 February 2005

 

Acta Cryst. (2005). D61, 350-354  [ doi:10.1107/S0907444904034389 ]

Unusual twinning in an acetyl coenzyme A synthetase (ADP-forming) from Pyrococcus furiosus

L. Lehtiö, I. Fabrichniy, T. Hansen, P. Schönheit and A. Goldman

Synopsis: Pseudo-merohedrally twinned crystals of an ADP-forming acetyl coenzyme A synthetase from P. furiosus have been produced.

Online 24 February 2005