Biological Crystallography

 

Acta Cryst. (2006). D62, 1435-1445  [ doi:10.1107/S0907444906037784 ]

Engineering the catalytic domain of human protein tyrosine phosphatase for structure-based drug discovery

A. G. Evdokimov, M. Pokross, R. Walter, M. Mekel, B. Cox, C. Li, R. Bechard, F. Genbauffe, R. Andrews, C. Diven, B. Howard, V. Rastogi, J. Gray, M. Maier and K. G. Peters

Synopsis: Structures of human protein tyrosine phosphatase catalytic domain complexed with inhibitors were determined at high resolution. Engineering of protein variants suitable for the purposes of rapid structure-based drug discovery is discussed.

PDB references: 2i3r, 2i3u, 2hc2, 2hc1, 2i4e, 2i5x, 2i4g and 2i4h

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1446-1452  [ doi:10.1107/S0907444906038121 ]

The open-access high-throughput crystallization facility at EMBL Hamburg

J. Mueller-Dieckmann

Synopsis: An automated high-throughput crystallization facility which is open to the general user community has been established at EMBL Hamburg. The facility provides more than 1000 initial crystallization conditions and the ability to design customized screens; it has the capacity to generate more than 100 96-well crystallization plates per day and to store and image up to 10 000 plates.

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1453-1457  [ doi:10.1107/S0907444906038212 ]

Structure of Mycobacterium tuberculosis thioredoxin C

G. Hall, M. Shah, P. A. McEwan, C. Laughton, M. Stevens, A. Westwell and J. Emsley

Synopsis: The 1.3 Å resolution crystal structure of M. tuberculosis thioredoxin C is reported, demonstrating a novel packing of five C-terminal residues in the active-site groove.

PDB reference: 2i1u

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1458-1465  [ doi:10.1107/S0907444906038303 ]

Structural comparison of differently glycosylated forms of acid--glucosidase, the defective enzyme in Gaucher disease

B. Brumshtein, M. R. Wormald, I. Silman, A. H. Futerman and J. L. Sussman

Synopsis: Crystals of native Cerezyme^® (acid--glucosidase), the enzyme used in enzyme-replacement therapy in Gaucher disease, were obtained and the threee-dimensional structure solved. A number of sugar residues bound to three asparagines via N-glycosylation could be observed in the structure, and new conoformations of loops controlling access to the active site were detected.

PDB reference: 2j25

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1466-1474  [ doi:10.1107/S0907444906038376 ]

Structure of Escherichia coli UDP-N-acetylmuramoyl:L-alanine ligase (MurC)

T. Deva, E. N. Baker, C. J. Squire and C. A. Smith

Synopsis: The crystal structure of E. coli UDP-N-acetylmuramoyl:L-alanine ligase (MurC) has been determined at 2.6 Å resolution by MAD.

PDB reference: 2f00

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1475-1483  [ doi:10.1107/S0907444906038534 ]

What can be done with a good crystal and an accurate beamline?

J. Wang, M. Dauter and Z. Dauter

Synopsis: S-SAD data from proteinase K at a wavelength of 0.98 Å with a Bijvoet ratio of 0.46% were successfully used for phasing of the macromolecular structure despite the presence of identifiable radiation-damage effects.

PDB reference: 2id8

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1484-1493  [ doi:10.1107/S090744490603890X ]

High-resolution structure of the p53 core domain: implications for binding small-molecule stabilizing compounds

W. C. Ho, C. Luo, K. Zhao, X. Chai, M. X. Fitzgerald and R. Marmorstein

Synopsis: The high-resolution structure of the mouse p53 core domain, alone and bound to small-molecule compounds, provides a molecular scaffold for the structure-based design of p53-stabilization compounds for development as possible therapeutic agents.

PDB references: 2ioi, 2ioo and 2iom

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1494-1501  [ doi:10.1107/S0907444906039199 ]

The 1.8 Å resolution structure of hydroxycinnamoyl-coenzyme A hydratase-lyase (HCHL) from Pseudomonas fluorescens, an enzyme that catalyses the transformation of feruloyl-coenzyme A to vanillin

P. M. Leonard, A. M. Brzozowski, A. Lebedev, C. M. Marshall, D. J. Smith, C. S. Verma, N. J. Walton and G. Grogan

Synopsis: The crystal structure of hydroxycinnamoyl-CoA hydratase-lyase (HCHL), the enzyme that catalyses the biotransformation of the coenzyme A thioester of ferulic acid [3-(4-hydroxy-3-methoxy-phenyl)prop-2-enoic acid] to vanillin (4-hydroxy-3-methoxy-benzaldehyde), has been solved and, in combination with a modelling study, a binding and discrimination mode for the substrate has been proposed.

PDB reference: 2j5i

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1502-1509  [ doi:10.1107/S0907444906039369 ]

Structure of the UNC5H2 death domain

N. Handa, M. Kukimoto-Niino, R. Akasaka, K. Murayama, T. Terada, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, E. Nunokawa, A. Tanaka, Y. Hayashizaki, T. Kigawa, M. Shirouzu and S. Yokoyama

Synopsis: The crystal structure of the mouse UNC5H2 death domain at 2.1 Å resolution is reported. The UNC5H2 death domain is a dimer in the crystal and in solution.

PDB reference: 1wmg

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1510-1519  [ doi:10.1107/S0907444906039850 ]

Structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA-aminoacylation and nuclear-export cofactor Arc1p reveal a novel function for an old fold

H. Simader, M. Hothorn and D. Suck

Synopsis: The heteromerization domain of the glutamyl-tRNA synthetase (GluRS) from yeast was crystallized and phase information was obtained from selenomethionine MAD data to 2.5 Å resolution. This structure and that of the interacting domain of Arc1p, a protein cofactor of GluRS, were refined to 1.9 Å resolution. Both domains adopt a GST-like fold, demonstrating a novel role for this fold as a protein-protein interaction domain.

PDB references: 2hra and 2hqt

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1520-1534  [ doi:10.1107/S0907444906040807 ]

Analysis of protein hydration in ultrahigh-resolution structures of the SRP GTPase Ffh

U. D. Ramirez and D. M. Freymann

Synopsis: Comparison of three 1.1 Å resolution structures of Ffh reveals conserved patterns of surface-water interactions that accommodate both protein structural plasticity and the disruption of the hydrogen-bonding network by bound solutes.

PDB references: 2j46 and 2j45

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1535-1544  [ doi:10.1107/S0907444906041035 ]

Ultrahigh-resolution study of protein atomic displacement parameters at cryotemperatures obtained with a helium cryostat

T. Petrova, S. Ginell, A. Mitschler, I. Hazemann, T. Schneider, A. Cousido, V. Y. Lunin, A. Joachimiak and A. Podjarny

Synopsis: Increasing the temperature of X-ray data collection from 15 to 60 K results in an almost constant increase (1.7 Å²) in isotropic equivalents B of atomic displacement parameters for atoms with B values below 8 Å².

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1545-1554  [ doi:10.1107/S0907444906041655 ]

Structure of the ribosomal protein L1-mRNA complex at 2.1 Å resolution: common features of crystal packing of L1-RNA complexes

S. Tishchenko, E. Nikonova, A. Nikulin, N. Nevskaya, S. Volchkov, W. Piendl, M. Garber and S. Nikonov

Synopsis: The crystal structure of ribosomal protein L1 in complex with a specific fragment of mRNA was solved at 2.1 Å resolution. Analysis of the crystal packing of L1-RNA complexes containing various 23S rRNA or mRNA fragments revealed a number of common features.

PDB reference: 2hw8

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1555-1563  [ doi:10.1107/S0907444906044489 ]

X-ray diffraction structure of a cell-wall invertase from Arabidopsis thaliana

M. Verhaest, W. Lammens, K. Le Roy, B. De Coninck, C. J. De Ranter, A. Van Laere, W. Van den Ende and A. Rabijns

Synopsis: The structure of A. thaliana cell-wall invertase 1 was determined to be an N-terminal fivefold -propeller domain followed by a C-terminal domain formed by two -sheets.

PDB reference: 2ac1

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1564-1570  [ doi:10.1107/S0907444906040169 ]

Molecular replacement in the `twilight zone': structure determination of the non-haem iron oxygenase NovR from Streptomyces spheroides through repeated density modification of a poor molecular-replacement solution

S. Keller, F. Pojer, L. Heide and D. M. Lawson

Synopsis: The crystal structure of NovR, a non-haem iron oxygenase from S. spheroides, was solved by molecular replacement with native X-ray data to 2.1 Å resolution using a template structure of relatively low sequence identity. An interpretable electron-density map was subsequently obtained from poor starting phases using a combination of fourfold averaging and very gradual phase extension.

Online 23 November 2006

 

Acta Cryst. (2006). D62, 1571  [ doi:10.1107/S0907444906044246 ]

Application of the use of high-throughput technologies to the determination of protein structures of bacterial and viral pathogens. Corrigendum

M. J. Fogg, P. Alzari, M. Bahar, I. Bertini, J.-M. Betton, W. P. Burmeister, C. Cambillau, B. Canard, M. A. Carrondo, M. Coll, S. Daenke, O. Dym, M.-P. Egloff, F. J. Enguita, A. Geerlof, A. Haouz, T. A. Jones, Q. Ma, S. N. Manicka, M. Migliardi, P. Nordlund, R. J. Owens, Y. Peleg, G. Schneider, R. Schnell, D. I. Stuart, N. Tarbouriech, T. Unge, A. J. Wilkinson, M. Wilmanns, K. S. Wilson, O. Zimhony and J. M. Grimes

Synopsis: A corrigendum to the paper by Fogg et al. (2006), Acta Cryst. D62, 1196-1207.

Online 23 November 2006