Biological Crystallography

 

Acta Cryst. (2006). D62, 947-952  [ doi:10.1107/S0907444906020063 ]

Structure of a calcium-deficient form of influenza virus neuraminidase: implications for substrate binding

B. J. Smith, T. Huyton, R. P. Joosten, J. L. McKimm-Breschkin, J.-G. Zhang, C. S. Luo, M.-Z. Lou, N. E. Labrou and T. P. J. Garrett

Synopsis: A crystal form of influenza virus neuraminidase isolated from whale is reported in which calcium ions are absent, leading to structural heterogeneity of loops near the enzyme active site. Sulfate ions are observed in and near the active site.

PDB reference: 2b8h

Online 19 August 2006

 

Acta Cryst. (2006). D62, 953-963  [ doi:10.1107/S0907444906020427 ]

Structure of a bovine secretory signalling glycoprotein (SPC-40) at 2.1 Å resolution

J. Kumar, A. S. Ethayathulla, D. B. Srivastava, S. Sharma, S. B. Singh, A. Srinivasan, M. P. Yadav and T. P. Singh

Synopsis: The crystal structure of a bovine secretory signalling glycoprotein (SPC-40) has been determined at 2.1 Å resolution. The structure reveals new features of the sugar-binding groove and the presence of a novel flexible region implicated as being involved in receptor recognition.

PDB reference: 2esc

Online 19 August 2006

 

Acta Cryst. (2006). D62, 964-970  [ doi:10.1107/S0907444906020592 ]

Structure of an ETHE1-like protein from Arabidopsis thaliana

J. G. McCoy, C. A. Bingman, E. Bitto, M. M. Holdorf, C. A. Makaroff and G. N. Phillips

Synopsis: The crystal structure of AtETHE1 has been solved to a resolution of 1.48 Å. The structure has been analyzed and comparison is made to previously published structures of glyoxalase II enzymes.

PDB reference: 2gcu

Online 19 August 2006

 

Acta Cryst. (2006). D62, 971-979  [ doi:10.1107/S0907444906020737 ]

Structure of the N-terminal domain of human CEACAM1: binding target of the opacity proteins during invasion of Neisseria meningitidis and N. gonorrhoeae

A. Fedarovich, J. Tomberg, R. A. Nicholas and C. Davies

Synopsis: The crystal structure of the N-terminal domain of human CEACAM1 is presented at 2.2 Å resolution. This structure is compared with its homologue from mouse and the binding surfaces are mapped for Neisseria Opa proteins and for other CEACAM molecules.

PDB reference: 2gk2

Online 19 August 2006

 

Acta Cryst. (2006). D62, 980-990  [ doi:10.1107/S0907444906021123 ]

Structure of conkunitzin-S1, a neurotoxin and Kunitz-fold disulfide variant from cone snail

C. Y. Dy, P. Buczek, J. S. Imperial, G. Bulaj and M. P. Horvath

Synopsis: Most Kunitz proteins like BPTI and -dendrotoxin are stabilized by three disulfide bonds. The crystal structure shows how subtle repacking of non-covalent interactions may compensate for disulfide bond loss in a naturally occurring two-disulfide variant, conkunitzin-S1, the first discovered member of a new conotoxin family.

PDB reference: 1y62

Online 19 August 2006

 

Acta Cryst. (2006). D62, 991-995  [ doi:10.1107/S0907444906020877 ]

Reproducible improvements in order and diffraction limit of crystals of bovine mitochondrial F₁-ATPase by controlled dehydration

M. W. Bowler, M. G. Montgomery, A. G. W. Leslie and J. E. Walker

Synopsis: The diffraction properties of crystals of bovine F₁-ATPase have been improved reproducibly by controlled dehydration, resulting in diffraction to 1.8 Å resolution.

Online 19 August 2006

 

Acta Cryst. (2006). D62, 996-1001  [ doi:10.1107/S0907444906021627 ]

An ensemble of crystallographic models enables the description of novel bromate-oxoanion species trapped within a protein crystal

J. Ondrácek and J. R. Mesters

Synopsis: The structure of a protein soaked in a bromate solution has been determined to a resolution of 1.25 Å.

PDB reference: 2d6b

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1002-1011  [ doi:10.1107/S0907444906022116 ]

The Buccaneer software for automated model building. 1. Tracing protein chains

K. Cowtan

Synopsis: A new technique for the automated tracing of protein chains in experimental electron-density maps is described. The technique relies on the application of an electron-density likelihood target function to identify likely candidate C positions and to then grow these into connected protein chains.

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1012-1021  [ doi:10.1107/S0907444906023158 ]

Identifying non-crystallographic symmetry in protein electron-density maps: a feature-based approach

R. Pai, J. Sacchettini and T. Ioerger

Synopsis: A robust, accurate and efficient feature-based algorithm to determine NCS operators in the initial stages of the structure determination process.

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1022-1029  [ doi:10.1107/S0907444906023638 ]

Structure of plastocyanin from the cyanobacterium Anabaena variabilis

L. Schmidt, H. E. M. Christensen and P. Harris

Synopsis: The crystal structure of the unique basic plastocyanin from A. variabilis was determined at 1.6 Å resolution.

PDB reference: 2gim

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1030-1038  [ doi:10.1107/S0907444906023869 ]

Quantifying X-ray radiation damage in protein crystals at cryogenic temperatures

J. Kmetko, N. S. Husseini, M. Naides, Y. Kalinin and R. E. Thorne

Synopsis: An experimental protocol is defined that provides a robust and reliable assessment of the radiation-sensitivity of protein crystals. Measurements on lysozyme crystals with varying heavy-ion content and on crystals of three other proteins suggest that radiation damage per dose is roughly constant at cryogenic temperatures.

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1039-1045  [ doi:10.1107/S0907444906023705 ]

Automated streak-seeding with micromachined silicon tools

A. Georgiev, S. Vorobiev, W. Edstrom, T. Song, A. Laine, J. Hunt and P. Allen

Synopsis: An automated robotic system for protein streak-seeding is described which uses novel silicon microtools in place of the commonly used boar bristles.

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1046-1057  [ doi:10.1107/S0907444906024541 ]

The cofactor-induced pre-active conformation in PhoB

M. Solà, D. L. Drew, A. G. Blanco, F. X. Gomis-Rüth and M. Coll

Synopsis: Mg²⁺ induces a flexible state in helix 4 at the PhoB receiver domain 4-5-5 surface.

PDB reference: 2yin

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1058-1065  [ doi:10.1107/S0907444906023821 ]

Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses

M. Hiraki, R. Kato, M. Nagai, T. Satoh, S. Hirano, K. Ihara, N. Kudo, M. Nagae, M. Kobayashi, M. Inoue, T. Uejima, S. Oda, L. M. G. Chavas, M. Akutsu, Y. Yamada, M. Kawasaki, N. Matsugaki, N. Igarashi, M. Suzuki and S. Wakatsuki

Synopsis: An automated large-scale protein-crystallization and monitoring system for high-throughput protein structural analyses has been developed. Many protein crystals have been obtained using the system.

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1066-1072  [ doi:10.1107/S090744490602614X ]

Integrated state evaluation for the images of crystallization droplets utilizing linear and nonlinear classifiers

K. Kawabata, K. Saitoh, M. Takahashi, M. Sugahara, H. Asama, T. Mishima and M. Miyano

Synopsis: The method presented here evaluates protein crystallization states using classifiers.

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1073-1084  [ doi:10.1107/S0907444906026333 ]

The 1.23 Å structure of Pichia pastoris lysyl oxidase reveals a lysine-lysine cross-link

A. P. Duff, A. E. Cohen, P. J. Ellis, K. Hilmer, D. B. Langley, D. M. Dooley, H. C. Freeman and J. M. Guss

Synopsis: The high-resolution structure of P. pastoris lysyl oxidase reveals a lysine-lysine cross-link presumed to result from autocatalytic oxidation of a lysine residue of the enzyme.

PDB reference: 1w7c

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1085-1097  [ doi:10.1107/S0907444906024826 ]

Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family

L. Arnfors, T. Hansen, P. Schönheit, R. Ladenstein and W. Meining

Synopsis: The crystal structures of the apo form and a complex of M. jannaschii nucleoside kinase have been solved at 1.7 and 1.9 Å resolution, respectively. Several structural features typical for proteins from hyperthermophilic organisms, such as increased charged and a decreased hydrophobic accessible surface area and a higher fraction of charged residues, ionic networks and large aromatic clusters, were identified.

PDB references: 2c4e and 2c49

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1098-1100  [ doi:10.1107/S090744490602244X ]

NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps

K. Suhre, J. Navaza and Y.-H. Sanejouand

Synopsis: This paper describes a freely available software suite that allows the modelling of large conformational changes of protein structures for the interpretation of electron-microscopy reconstructions.

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1101  [ doi:10.1107/S0907444906023766 ]

Structural Aspects of Protein Synthesis

Online 19 August 2006

 

Acta Cryst. (2006). D62, 1102  [ doi:10.1107/S0907444906024073 ]

Applications of single-wavelength anomalous dispersion at high and atomic resolution. Corrigendum

D. E. Brodersen, E. de La Fortelle, C. Vonrhein, G. Bricogne, J. Nyborg and M. Kjeldgaard

Synopsis: A corrigendum to the paper by Brodersen et al. (2000), Acta Cryst. D56, 431-441.

Online 19 August 2006