Biological Crystallography

 

Acta Cryst. (2006). D62, 569-575  [ doi:10.1107/S0907444906012601 ]

Crystallization to obtain protein-ligand complexes for structure-aided drug design

D. E. Danley

Synopsis: This article reviews the issues, methods and strategies involved in obtaining the crystals of protein-ligand complexes that are critical for structure-aided drug design.

Online 12 May 2006

 

Acta Cryst. (2006). D62, 576-581  [ doi:10.1107/S0907444906011887 ]

The high-resolution structure of (+)-epi-biotin bound to streptavidin

I. Le Trong, D. G. L. Aubert, N. R. Thomas and R. E. Stenkamp

Synopsis: A high-resolution structure determination shows that (+)-epi-biotin and (+)-biotin bind similarly to streptavidin by using conformational changes in their tetrahydrothiophene rings to accommodate their different configurations at the C2 carbon.

PDB references: 2gh7 and 2f01

Online 12 May 2006

 

Acta Cryst. (2006). D62, 582-588  [ doi:10.1107/S0907444906010109 ]

Structure of human DSP18, a member of the dual-specificity protein tyrosine phosphatase family

D. G. Jeong, Y. H. Cho, T.-S. Yoon, J. H. Kim, J. H. Son, S. E. Ryu and S. J. Kim

Synopsis: The crystal structure of human dual-specificity protein tyrosine phosphatase 18 provides the structural basis for the unusual catalytic activity at high temperature.

PDB reference: 2esb

Online 12 May 2006

 

Acta Cryst. (2006). D62, 589-594  [ doi:10.1107/S0907444906010456 ]

Structural elucidation of the PDI-related chaperone Wind with the help of mutants

M. Sevvana, M. Biadene, Q. Ma, C. Guo, H.-D. Söling, G. M. Sheldrick and D. M. Ferrari

Synopsis: The structures of the PDI-related protein Wind and three mutants show the same mode of dimerization and only subtle differences in the putative Pipe-binding region, although two of the mutants completely abrogate Pipe transport.

PDB references: 2c0e, 2c0f, 2c0g and 2c1y

Online 12 May 2006

 

Acta Cryst. (2006). D62, 595-604  [ doi:10.1107/S0907444906010687 ]

Structure of recombinant Ves v 2 at 2.0 Å resolution: structural analysis of an allergenic hyaluronidase from wasp venom

L. K. Skov, U. Seppälä, J. J. F. Coen, N. Crickmore, T. P. King, R. Monsalve, J. S. Kastrup, M. D. Spangfort and M. Gajhede

Synopsis: This paper describes the production and structural characterization of the allergen Ves v 2 from wasp venom. Implications for cross-reactivity are discussed.

PDB reference: 2atm

Online 12 May 2006

 

Acta Cryst. (2006). D62, 605-612  [ doi:10.1107/S0907444906011735 ]

A survey of protein-protein complex crystallizations

S. Radaev, S. Li and P. D. Sun

Synopsis: A survey of crystallization conditions was carried out for all known protein-protein complexes to define the boundaries of their configuration space. Based on the survey, a probability-based sparse-matrix screen and a systematic buffer and pH screen are proposed to facilitate the crystallization of protein-protein complexes.

Online 12 May 2006

 

Acta Cryst. (2006). D62, 613-618  [ doi:10.1107/S0907444906009474 ]

Mapping the active site of Escherichia coli malonyl-CoA-acyl carrier protein transacylase (FabD) by protein crystallography

C. Oefner, H. Schulz, A. D'Arcy and G. E. Dale

Synopsis: Various binary complex structures of E. coli malonyl-CoA-acyl carrier protein transacylase are presented, including that of the natural substrate malonyl-CoA. Based on the presented structural data, a possible new catalytic enzyme mechanism is discussed.

PDB references: 2g1h, 2g2o, 2g2y and 2g2z

Online 12 May 2006

 

Acta Cryst. (2006). D62, 619-627  [ doi:10.1107/S0907444906012388 ]

Novel crystal form of the ColE1 Rom protein

S. B. Jang, M. S. Jeong, R. J. Carter, E. L. Holbrook, L. R. Comolli and S. R. Holbrook

Synopsis: The structure of Rom has been determined in a new crystal form from X-ray diffraction data to 2.5 Å resolution.

PDB reference: 2ghy

Online 12 May 2006

 

Acta Cryst. (2006). D62, 628-638  [ doi:10.1107/S0907444906012728 ]

Invariance and variability in bacterial PanK: a study based on the crystal structure of Mycobacterium tuberculosis PanK

S. Das, P. Kumar, V. Bhor, A. Surolia and M. Vijayan

Synopsis: The structure of a complex of M. tuberculosis pantothenate kinase with a coenzyme A derivative has been determined in two crystal forms, each at two temperatures. The structure and a comparative analysis involving the known structure of the E. coli enzyme and the sequences of the enzyme from other bacteria show a strong correlation among structural plasticity, evolutionary relatedness and function.

PDB references: 2ges, 2get, 2geu and 2gev

Online 12 May 2006

 

Acta Cryst. (2006). D62, 639-647  [ doi:10.1107/S0907444906013072 ]

Interaction energies between glycopeptide antibiotics and substrates in complexes determined by X-ray crystallography: application of a theoretical databank of aspherical atoms and a symmetry-adapted perturbation theory-based set of interatomic potentials

X. Li, A. V. Volkov, K. Szalewicz and P. Coppens

Synopsis: Intermolecular interaction energies between fragments of glycopeptide antibiotics and small peptide ligands are evaluated using X-ray geometries and new methods, suitable for application to very large molecular complexes. The calculation of the electrostatic contributions is based on charge densities constructed with a databank of transferable aspherical atoms, whereas non-electrostatic contributions are evaluated with a new set of atom-atom potentials fitted to symmetry-adapted perturbation-theory results.

Online 12 May 2006

 

Acta Cryst. (2006). D62, 648-658  [ doi:10.1107/S0907444906013333 ]

MUMBO: a protein-design approach to crystallographic model building and refinement

M. T. Stiebritz and Y. A. Muller

Synopsis: Upon introduction of an X-ray pseudo-energy derived from the electron density present at a specific protein residue, protein design algorithms can be used readily for crystallographic model building and refinement purposes.

Online 12 May 2006

 

Acta Cryst. (2006). D62, 659-664  [ doi:10.1107/S090744490601359X ]

The first crystal structure of an RNA racemate

W. Rypniewski, M. Vallazza, M. Perbandt, S. Klussmann, L. J. DeLucas, C. Betzel and V. A. Erdmann

Synopsis: The racemate of the RNA duplex r(CUGGGCGG)·r(CCGCCUGG) crystallizes with L-duplexes and D-duplexes stacked end-to-end in a centrosymmetric lattice.

PDB references: 2g32, 2gq4, 2gpm, 2gq5, 2gq6 and 2gq7

Online 12 May 2006

 

Acta Cryst. (2006). D62, 665-670  [ doi:10.1107/S0907444906011693 ]

Multiple crystal forms of the cell-wall invertase inhibitor from tobacco support high conformational rigidity over a broad pH range

M. Hothorn and K. Scheffzek

Synopsis: The structure of the plant invertase inhibitor Nt-CIF from tobacco has been determined in six independent crystal forms covering pH 4.6-9.5.

PDB references: 2cj4, 2cj5, 1rj1, 1rj4, 2cj6, 2cj7 and 2cj8

Online 12 May 2006

 

Acta Cryst. (2006). D62, 671-677  [ doi:10.1107/S0907444906013813 ]

High-resolution structure of human cytoglobin: identification of extra N- and C-termini and a new dimerization mode

M. Makino, H. Sugimoto, H. Sawai, N. Kawada, K. Yoshizato and Y. Shiro

Synopsis: The high-resolution structure of a new crystal form of human cytoglobin has been determined, revealing an additional helix in the N-terminus and a new dimeric arrangement.

PDB reference: 2dc3

Online 12 May 2006

 

Acta Cryst. (2006). D62, 678-682  [ doi:10.1107/S0907444906014594 ]

Small revisions to predicted distances around metal sites in proteins

M. M. Harding

Synopsis: Revisions are based on structures now in the Protein Data Bank with resolution 1.25 Å, as well as small-molecule structures in the Cambridge Structural Database; patterns shown in bidentate carboxylates are explored.

Online 12 May 2006

 

Acta Cryst. (2006). D62, 683-686  [ doi:10.1107/S0907444906014107 ]

Structure determination and analysis of acyl-CoA oxidase (ACX1) from tomato

R. A. Powers, C. L. Rife, A. L. Schilmiller, G. A. Howe and R. M. Garavito

Synopsis: The crystal structure of LeACX1 from tomato was determined to 2.74 Å resolution. The packing arrangement observed was unusual, containing three monomers in the asymmetric unit: the biological dimer plus a half dimer.

PDB reference: 2fon

Online 12 May 2006