Biological Crystallography

 

Acta Cryst. (2008). D64, 227-236  [ doi:10.1107/S0907444907065572 ]

Modulation of activity by Arg407: structure of a fungal -1,2-mannosidase in complex with a substrate analogue

Y. D. Lobsanov, T. Yoshida, T. Desmet, W. Nerinckx, P. Yip, M. Claeyssens, A. Herscovics and P. L. Howell

Synopsis: The structure of P. citrinum -1,2-mannosidase has been determined at 1.95 Å resolution in complex with methyl--D-lyxopyranosyl-(1',2)--D-mannopyranoside.

PDB references: 2ri8 and 2ri9

Online 20 February 2008

 

Acta Cryst. (2008). D64, 237-247  [ doi:10.1107/S0907444907065663 ]

Application of maximum-entropy maps in the accurate refinement of a putative acylphosphatase using 1.3 Å X-ray diffraction data

E. Nishibori, T. Nakamura, M. Arimoto, S. Aoyagi, H. Ago, M. Miyano, T. Ebisuzaki and M. Sakata

Synopsis: An accurate structural refinement using the maximum-entropy method (MEM) is reported. The reliability factor R_free in the SHELX refinement was reduced from 18% to 10% by model building based on MEM charge densities.

Online 20 February 2008

 

Acta Cryst. (2008). D64, 248-256  [ doi:10.1107/S0907444907065766 ]

Three-dimensional structures of L-asparaginase from Erwinia carotovora complexed with aspartate and glutamate

O. V. Kravchenko, Y. A. Kislitsin, A. N. Popov, S. V. Nikonov and I. P. Kuranova

Synopsis: L-Asparaginase from Er. carotovora belongs to the family of bacterial amidohydrolases and catalyzes the conversion of L-asparagine to aspartic acid and ammonia and, to a lesser extent, the formation of L-glutamic acid from L-glutamine. The highly homologous L-asparaginases from E. coli and Er. chrysanthemi are widely used as effective anti-leukaemia drugs. Like the majority of L-asparaginases, ErcA also reveals antitumour activity, but differs from EcA and ErchA in antigenic specificity. Therefore, ErcA is of special interest as a potential therapeutic agent and as an enzyme suitable for drug development.

PDB references: 2gvn and 2hln

Online 20 February 2008

 

Acta Cryst. (2008). D64, 257-263  [ doi:10.1107/S090744490706595X ]

Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination

I. Dokmanic, M. Sikic and S. Tomic

Synopsis: A study of the specificities of divalent metal cation-binding sites in proteins with known three-dimensional structure is presented.

Online 20 February 2008

 

Acta Cryst. (2008). D64, 264-272  [ doi:10.1107/S0907444907065948 ]

Differential specific radiation damage in the Cu^II-bound and Pd^II-bound forms of an -helical foldamer: a case study of crystallographic phasing by RIP and SAD

K. Fütterer, R. B. G. Ravelli, S. A. White, A. J. Nicoll and R. K. Allemann

Synopsis: Radiation-damage-induced phasing of Pd^II-bound and Cu^II-bound complexes of an 18-residue peptide with two disulfide bonds derived from the neurotoxin apamin rested on the differential susceptibility of radiation-sensitive groups in non-isomorphous lattices.

Online 20 February 2008

 

Acta Cryst. (2008). D64, 273-278  [ doi:10.1107/S0907444907066164 ]

Structure of human monocyte chemoattractant protein 4 (MCP-4/CCL13)

C. Barinka, A. Prahl and J. Lubkowski

Synopsis: The crystal structure of human monocyte chemoattractant protein 4 (MCP-4), a member of the CC chemokine family, has been determined at 1.70 Å resolution.

PDB reference: 2ra4

Online 20 February 2008

 

Acta Cryst. (2008). D64, 279-286  [ doi:10.1107/S0907444907067455 ]

Structure of human argininosuccinate synthetase

T. Karlberg, R. Collins, S. van den Berg, A. Flores, M. Hammarström, M. Högbom, L. Holmberg Schiavone and J. Uppenberg

Synopsis: The first crystal structure of human argininosuccinate synthetase is presented and is compared with its bacterial counterparts.

PDB reference: 2nz2

Online 20 February 2008

 

Acta Cryst. (2008). D64, 287-301  [ doi:10.1107/S0907444907067613 ]

Glycerol concentrations required for the successful vitrification of cocktail conditions in a high-throughput crystallization screen

R. Kempkes, E. Stofko, K. Lam and E. H. Snell

Synopsis: The glycerol concentrations necessary to vitrify 1536 high-throughput crystallization-screening cocktails have been determined in order to aid rational prioritization of crystallization leads observed in these cocktails. The concentrations were made by dilution rather than by the replacement of water with glycerol. They therefore serve as a worst-case scenario.

Online 20 February 2008

 

Acta Cryst. (2008). D64, 302-308  [ doi:10.1107/S0907444907067844 ]

Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester

R. Hayouka, Y. Eisenberg-Domovich, V. P. Hytönen, J. A. E. Määttä, H. R. Nordlund, M. S. Kulomaa, M. Wilchek, E. A. Bayer and O. Livnah

Synopsis: Combined mutagenesis and X-ray analysis have been used to attempt to understand the diametric difference in the biotin-binding properties of avidin and streptavidin.

PDB references: 2of8, 2of9, 2ofa and 2ofb

Online 20 February 2008

 

Acta Cryst. (2008). D64, 309-320  [ doi:10.1107/S0907444907068072 ]

Crystal packing of plant-type L-asparaginase from Escherichia coli

K. Michalska, D. Borek, A. Hernández-Santoyo and M. Jaskolski

Synopsis: Several crystal forms of E. coli asparaginase/isoaspartyl peptidase (EcAIII) can be obtained under essentially the same crystallization conditions. They all have P2₁2₁2₁ symmetry with similar unit-cell parameters, but show non-isomorphous crystal packing.

PDB reference: 2zak

Online 20 February 2008

 

Acta Cryst. (2008). D64, 321-330  [ doi:10.1107/S0907444907068552 ]

The structure of a redundant enzyme: a second isoform of aspartate -semialdehyde dehydrogenase in Vibrio cholerae

R. E. Viola, X. Liu, J. F. Ohren and C. R. Faehnle

Synopsis: The structure of a second form of aspartate semialdehyde dehydrogenase from V. cholerae has been determined from crystals grow through optimization of the starting buffer conditions. The similarities and differences between isoforms are discussed from both a structural and a functional perspective.

PDB references: 2qz9 and 2r00

Online 20 February 2008

 

Acta Cryst. (2008). D64, 331-334  [ doi:10.1107/S0907444907067479 ]

Structures of D-amino-acid amidase complexed with L-phenylalanine and with L-phenylalanine amide: insight into the D-stereospecificity of D-amino-acid amidase from Ochrobactrum anthropi SV3

S. Okazaki, A. Suzuki, T. Mizushima, H. Komeda, Y. Asano and T. Yamane

Synopsis: The crystal structures of D-amino acid amidase complexed with L-phenylalanine and with L-phenylalanine amide reveal three factors related to its D-stereospecificity.

PDB references: 2efu and 2efx

Online 20 February 2008

 

Acta Cryst. (2008). D64, 335-336  [ doi:10.1107/S0907444908002333 ]

A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions

P. A. Karplus, M. V. Shapovalov, R. L. Dunbrack and D. S. Berkholz

Synopsis: A suggestion is put forward concerning the stereochemical restraints debate.

Online 20 February 2008