Biological Crystallography

Acta Cryst. (2011). D67, 671-677  [ doi:10.1107/S090744491101746X ]

Structural and kinetic insights into the mechanism of 5-hydroxyisourate hydrolase from Klebsiella pneumoniae

J. B. French and S. E. Ealick

Synopsis: The crystal structure of 5-hydroxyisourate hydrolase from K. pneumoniae and the steady-state kinetic parameters of the native enzyme as well as several mutants provide insights into the catalytic mechanism of this enzyme and the possible roles of the active-site residues.

PDB reference: 3qva

Online 12 July 2011

Acta Cryst. (2011). D67, 678-689  [ doi:10.1107/S0907444911021834 ]

Structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae

K. Michalska, M. E. Cuff, C. Tesar, B. Feldmann and A. Joachimiak

Synopsis: The crystal structure of 2-oxo-3-deoxygalactonate kinase from the De Ley-Doudoroff pathway of galactose metabolism has been determined at 2.1 Å resolution.

PDB reference: 3r1x

Online 12 July 2011

Acta Cryst. (2011). D67, 690-698  [ doi:10.1107/S0907444911022463 ]

Structural features of peroxisomal catalase from the yeast Hansenula polymorpha

E. Peña-Soler, M. C. Vega, M. Wilmanns and C. Williams

Synopsis: This study presents the crystal structure of catalase from the thermotolerant yeast H. polymorpha at 2.9 Å resolution.

PDB reference: 2xq1

Online 12 July 2011

Acta Cryst. (2011). D67, 699-706  [ doi:10.1107/S090744491102292X ]

A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution

D. E. Tronrud and P. A. Karplus

Synopsis: A script was created to allow SHELXL to use the new CDL v.1.2 stereochemical library which defines the target values for main-chain bond lengths and angles as a function of the residue's / angles. Test refinements using this script show that the refinement behavior of structures at resolutions even better than 1 Å is substantially enhanced by the use of the new conformation-dependent ideal geometry paradigm.

Online 12 July 2011

Acta Cryst. (2011). D67, 707-715  [ doi:10.1107/S0907444911023821 ]

Structural and biochemical characterization of N⁵-carboxyaminoimidazole ribonucleotide synthetase and N⁵-carboxyaminoimidazole ribonucleotide mutase from Staphylococcus aureus

P. Brugarolas, E. M. Duguid, W. Zhang, C. B. Poor and C. He

Synopsis: Purine biosynthesis is considered to be a promising new antibiotic target; in this article, the structural and biochemical characterization of S. aureus PurK and PurE are described.

PDB references: 3orq, 3orr and 3ors

Online 12 July 2011

Acta Cryst. (2011). D67, 716-728  [ doi:10.1107/S0907444911024024 ]

A unified convention for biological assemblies with helical symmetry

C.-J. Tsai and R. Nussinov

Synopsis: A new representation of helical structure by four parameters, [n₁, n₂, twist, rise], is able to generate an entire helical construct from asymmetric units, including cases of helical assembly with a seam.

Online 12 July 2011

Acta Cryst. (2011). D67, 729-738  [ doi:10.1107/S0907444911024887 ]

On the routine use of soft X-rays in macromolecular crystallography. Part V. Molecular replacement and anomalous scattering

J. Unge, C. Mueller-Dieckmann, S. Panjikar, P. A. Tucker, V. S. Lamzin and M. S. Weiss

Synopsis: The performance of molecular-replacement approaches can be enhanced by utilizing anomalous differences and substructure information.

Online 12 July 2011

Acta Cryst. (2011). D67, 739-741  [ doi:10.1107/S090744491102258X ]

On the application of structure-specific bulk-solvent models

N. M. Glykos

Synopsis: Application of a highly detailed model for the bulk solvent obtained from molecular-dynamics simulations shows an improvement of the totally cross-validated free R value of only 0.3%.

Online 12 July 2011

Acta Cryst. (2011). D67, 742-744  [ doi:10.1107/S0907444911022803 ]

Distinguishing between Cl^- and O₂^2- as the bridging element between Fe³⁺ and Cu²⁺ in resting-oxidized cytochrome c oxidase

M. Suga, N. Yano, K. Muramoto, K. Shinzawa-Itoh, T. Maeda, E. Yamashita, T. Tsukihara and S. Yoshikawa

Synopsis: An anomalous dispersion analysis was performed in order to conclusively demonstrate the absence of Cl^- between the Fe³⁺ and Cu²⁺ in resting-oxidized cytochrome c oxidase.

PDB references: 3asn and 3aso

Online 12 July 2011

Acta Cryst. (2011). D67, 745  [ doi:10.1107/S0907444911026631 ]

Processing incommensurately modulated protein diffraction data with Eval15. Corrigendum

J. Porta, J. J. Lovelace, A. M. M. Schreurs, L. M. J. Kroon-Batenburg and G. E. O. Borgstahl

Synopsis: A correction to the article by Porta et al. [(2011). Acta Cryst. D67, 628-638].

Online 12 July 2011