Biological Crystallography

 

Acta Cryst. (2005). D61, 1  [ doi:10.1107/S0907444904032548 ]

Redefining Acta D

E. N. Baker and Z. Dauter

Online 17 December 2004

 

Acta Cryst. (2005). D61, 2-13  [ doi:10.1107/S0907444904025697 ]

Real-space protein-model completion: an inverse-kinematics approach

H. van den Bedem, I. Lotan, J.-C. Latombe and A. M. Deacon

Synopsis: A new algorithm to automatically fit a main-chain fragment to the electron density between two anchoring residues is presented. Examples of applications of the algorithm to the completion of initial protein models are included.

Online 17 December 2004

 

Acta Cryst. (2005). D61, 14-21  [ doi:10.1107/S0907444904025703 ]

Structure of an excitatory insect-specific toxin with an analgesic effect on mammals from the scorpion Buthus martensii Karsch

C. Li, R.-J. Guan, Y. Xiang, Y. Zhang and D.-C. Wang

Synopsis: The crystal structure of an excitatory insect-specific toxin, BmK IT-AP, from the scorpion B. martensii Karsch determined at 2.6  Å resolution showed an extension and `wiggling' of the C-terminal segment (residues 59-72) with an additional one-and-a-half turn -helix (2) and a shifted disulfide bridge Cys38-Cys64 in comparison with the mammal-selective BmK -toxins.

PDB reference: 1t0z

Online 17 December 2004

 

Acta Cryst. (2005). D61, 22-32  [ doi:10.1107/S0907444904025715 ]

Binding of N-acetylglucosamine oligosaccharides to hen egg-white lysozyme: a powder diffraction study

R. B. Von Dreele

Synopsis: High-resolution synchrotron X-ray powder diffraction data were used to determine binding modes for five N-acetylglucosamine oligosaccharides (NAG_n, n = 2-6) on HEW lysozyme.

PDB references: 1sf4, 1sf6, 1sf7, 1sfb and 1sfg

Online 17 December 2004

 

Acta Cryst. (2005). D61, 33-44  [ doi:10.1107/S0907444904025855 ]

Influence of multiple well defined conformations on small-angle scattering of proteins in solution

W. T. Heller

Synopsis: The influence of sampling a population of well defined protein conformations by small-angle scattering and subsequent data analysis is explored. The results demonstrate how the ensemble of well defined protein structures sampled influences the structural parameters and low-resolution models derived from the data.

Online 17 December 2004

 

Acta Cryst. (2005). D61, 45-52  [ doi:10.1107/S0907444904025971 ]

The identification of isoprenoids that bind in the intersubunit cavity of Escherichia coli 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase by complementary biophysical methods

L. E. Kemp, M. S. Alphey, C. S. Bond, M. A. J. Ferguson, S. Hecht, A. Bacher, W. Eisenreich, F. Rohdich and W. N. Hunter

Synopsis: New crystal forms of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase displayed electron density within an intersubunit cavity suggestive of an isoprenoid ligand. Mass spectrometry identified a mixture of ligands, the most abundant of which, geranyl diphosphate, was satisfactorily modelled in the binding sites. These ligands are produced downstream of this synthase in the non-mevalonate biosynthetic route to isoprenoids, suggesting the possibility of feedback regulation of this key metabolic pathway.

PDB references: 1h47 and 1h48

Online 17 December 2004

 

Acta Cryst. (2005). D61, 53-59  [ doi:10.1107/S0907444904026009 ]

Effects of the silanized mica surface on protein crystallization

L. Tang, Y. B. Huang, D. Q. Liu, J. L. Li, K. Mao, L. Liu, Z. J. Cheng, W. M. Gong, J. Hu and J. H. He

Synopsis: The effects of the silanized mica surface on protein crystallization have been investigated in the paper. It has been found that this silanized mica surface can ameliorate crystallization process considerably and improve the diffraction ability of crystals compared with the silanized glass cover slip.

Online 17 December 2004

 

Acta Cryst. (2005). D61, 60-66  [ doi:10.1107/S0907444904026538 ]

An ultraviolet fluorescence-based method for identifying and distinguishing protein crystals

R. A. Judge, K. Swift and C. González

Synopsis: Protein crystals can be clearly imaged and distinguished from non-protein crystals using the intrinsic ultraviolet fluorescence of these macromolecules. The method is fast and non-invasive and therefore well suited to the needs of high-throughput crystallography.

Online 17 December 2004

 

Acta Cryst. (2005). D61, 67-74  [ doi:10.1107/S0907444904026721 ]

Correction of X-ray intensities from single crystals containing lattice-translocation defects

J. Wang, S. Kamtekar, A. J. Berman and T. A. Steitz

Synopsis: The random translocation of layers within a single crystal modulates observed intensities. A general forumla is proposed for solving this 50-year old problem.

Online 17 December 2004

 

Acta Cryst. (2005). D61, 75-79  [ doi:10.1107/S0907444904026964 ]

The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens

P. A. Williams, L. Coates, F. Mohammed, R. Gill, P. T. Erskine, A. Coker, S. P. Wood, C. Anthony and J. B. Cooper

Synopsis: The crystal structure of methanol dehydrogenase (MDH) from Methylobacterium extorquens has been refined without stereochemical restraints at a resolution of 1.2  Å. The high-resolution data have defined the conformation of the tricyclic pyrroloquinoline quinone (PQQ) cofactor ring as entirely planar.

PDB reference: 1w6s

Online 17 December 2004

 

Acta Cryst. (2005). D61, 80-87  [ doi:10.1107/S0907444904027179 ]

Pros and cons of cryocrystallography: should we also collect a room-temperature data set?

K. V. Dunlop, R. T. Irvin and B. Hazes

Synopsis: Cryogenic structures show systematic alterations from room-temperature structures. These cryoinduced structural changes include more extensive hydration, fewer disordered side chains, small coordinate shifts in the structural core and more extensive coordinate shifts at the protein surface.

PDB references: 1x6z, 1x6x, 1x6q, 1x6p, 1x6r and 1x6y

Online 17 December 2004

 

Acta Cryst. (2005). D61, 88-98  [ doi:10.1107/S0907444904027325 ]

Protein imperfections: separating intrinsic from extrinsic variation of torsion angles

G. L. Butterfoss, J. S. Richardson and J. Hermans

Synopsis: In this paper, the variation of the values of dihedral angles in proteins is divided into two categories by analyzing distributions in a database of structures determined at a resolution of 1.8  Å or better.

Online 17 December 2004

 

Acta Cryst. (2005). D61, 99-107  [ doi:10.1107/S0907444904028173 ]

Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass

O. Pasternak, J. Biesiadka, R. Dolot, L. Handschuh, G. Bujacz, M. M. Sikorski and M. Jaskolski

Synopsis: The structure of a pathogenesis-related PR-10 protein from a novel yellow lupin subclass confirms the general fold of this group of proteins, with a cavity within the protein core. The structure suggests that a segment of a long C-terminal -helix characterized by low sequence conservation is involved in regulating the shape and size of the cavity, thus underlying the specificity of different PR-10 proteins towards their potential ligands.

PDB reference: 1xdf

Online 17 December 2004

 

Acta Cryst. (2005). D61, 108-111  [ doi:10.1107/S0907444904026800 ]

Going soft and SAD with manganese

P. S. Salgado, M. A. Walsh, M. R. L. Laurila, D. I. Stuart and J. M. Grimes

Synopsis: Manganese phasing of a 225  kDa protein asymmetric unit is reported, demonstrating that, with modern synchrotron beamlines and software, very small anomalous signals from light metals, such as manganese, provide a practical tool for solving the structure of large proteins.

Online 17 December 2004

 

Acta Cryst. (2005). D61, 112-116  [ doi:10.1107/S0907444904027684 ]

WHEATSHEAF: an algorithm to average protein structure ensembles

D. Thomas and A. Pastore

Synopsis: Thomas and Pastore describe a new algorithm that creates a single structure to represent ensembles produced by nuclear magnetic resonance spectroscopy or simulations of molecular dynamics.

Online 17 December 2004

 

Acta Cryst. (2005). D61, 117-122  [ doi:10.1107/S0907444904033086 ]

Notes for authors 2005

Online 17 December 2004