August 2008 issue
Cover illustration: Examples of recently remediated PDB entries with regular noncrystallographic symmetry (p. 874). Top left: yellow mottle virus (1f2n); top right: rhinovirus (4rhv); bottom left: pneumolysin (2bk1); center right: tobacco mosaic virus coat protein aggregate (1ei7); bottom right: cucumber green mottle mosaic virus (1cgm).
Acta Cryst. (2008). D64, 815-822
Crystal structures of urate oxidase from A. globiformis and of its complexes with uric acid, allantoate and 8-azaxanthin demonstrate details of substrate recognition and catalysis.
Acta Cryst. (2008). D64, 823-833
Improved classification of images from crystallization experiments is obtained using multiple classifiers to combine different feature-extraction methods.
Acta Cryst. (2008). D64, 834-842
A pattern-recognition-based method for the identification of planar objects in crystallographic electron-density maps is presented. The accuracy of the located centres of the planes is of the order of 0.5 Å.
Acta Cryst. (2008). D64, 843-850
Structure determination of the 1918 H1N1 neuraminidase from a crystal with lattice-translocation defects
The structure of the 1918 H1N1 neuraminidase was determined to 1.65 Å from crystals with a lattice-translocation defect using uncorrected, as well as corrected, diffraction data.
PDB reference: 1918 H1N1 neuraminidase, 3cye, r3cyesf
Acta Cryst. (2008). D64, 851-863
The short hydrogen bonds in rhamnogalacturonan acetylesterase have been investigated by structure determination of an active-site mutant, 1H NMR spectra and computational methods. Comparisons are made to database statistics. A very short carboxylic acid carboxylate hydrogen bond, buried in the protein, could explain the low-field (18 p.p.m.) 1H NMR signal.
PDB reference: D192N rhamnogalacturonan acetylesterase, 3c1u, r3c1usf
Acta Cryst. (2008). D64, 864-873
A novel phasing method that uses the charge-flipping algorithm has been used to solve the ab initio structure of biological macromolecules at atomic resolution and to determine heavy-atom or anomalous scattering substructures.
Acta Cryst. (2008). D64, 874-882
A new data model for PDB entries of viruses and other biological assemblies with regular noncrystallographic symmetry is described.
Acta Cryst. (2008). D64, 883-891
Structures of grape dihydroflavonol 4-reductase in complex with NADP+ and various flavonols suggest possible inhibition of the enzyme by flavonols. Initial kinetics experiments confirmed the inhibition and showed its competitive character.
PDB references: grape dihydroflavonol 4-reductase, 3bxx, r3bxxsf; 3c1t, r3c1tsf
Acta Cryst. (2008). D64, 892-901
Structural insights were obtained into the copper-chelation mechanism in superoxide dismutases.
PDB reference: superoxide dismutase, 2q2l, r2q2lsf
Acta Cryst. (2008). D64, 902-904
Two crystal structures of rhodopsin that were originally described using trigonal symmetry can be interpreted in a hexagonal unit cell with a smaller asymmetric unit.
PDB references: rhodopsin, ground state, 3c9l, 3c9lsf; mutant, 3c9m, 3c9msf
Acta Cryst. (2008). D64, 905-908
Coulombic and dispersive factors in the molecular recognition of peptides: PIXEL calculations on two NNQQ (Asn-Asn-Gln-Gln) crystal polymorphs
The crystal-packing and cohesive energies in the structures of two polymorphs of the title tetrapeptide have been analyzed using molecule–molecule energies calculated using the PIXEL method.