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

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.

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

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.

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

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

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

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.

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

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

A survey of protein–protein complex crystallizations

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.

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

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.

Novel crystal form of the ColE1 Rom protein

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

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

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.

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

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.

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

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.

The first crystal structure of an RNA racemate

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.

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

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.

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

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.

Small revisions to predicted distances around metal sites in proteins

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.

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

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.