Gary L. Gilliland

The Protein Data Bank

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

The Protein Data Bank and the Challenge of Structural Genomics

The PDB has created systems for the processing, exchange, query, and distribution of data that will enable many aspects of high throughput structural genomics.

The Protein Data Bank: unifying the archive

The Protein Data Bank (PDB; http://www.pdb.org/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the progress that has been made in validating all data in the PDB archive and in releasing a uniform archive for the community. We have now produced a collection of mmCIF data files for the PDB archive (ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/). A utility application that converts the mmCIF data files to the PDB format (called CIFTr) has also been released to provide support for existing software.

Structure of form III crystals of bovine pancreatic trypsin inhibitor.

The structure of bovine pancreatic trypsin inhibitor has been solved in a new crystal form III. The crystals belong to space group P2(1)2(1)2 with a = 55.2 A, b = 38.2 A, c = 24.05 A. The structure was solved on the basis of co-ordinates of forms I and II of the inhibitor by molecular replacement, and the X-ray data extending to 1.7 A were used in a restrained least-squares refinement. The final R factor was 0.16, and the deviation of bonded distances from ideality was 0.020 A. Root-mean-square discrepancy between C alpha co-ordinates of forms III and I are 0.47 A, whilst between forms II and III the discrepancy is 0.39 A. These deviations are about a factor of 3 larger than the expected experimental errors, showing that true differences exist between the three crystal forms. Two residues (Arg39 and Asp50) were modeled with two positions for their side-chains. The final model includes 73 water molecules and one phosphate group bound to the protein. Sixteen water molecules occupy approximately the same positions in all three crystal forms studied to date, indicating their close association with the protein molecule. Temperature factors also show a high degree of correlation between the three crystal forms.

Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase

BACKGROUND Feedback inhibition of biosynthetic threonine deaminase (TD) from Escherichia coli provided one of the earliest examples of protein-based metabolic regulation. Isoleucine, the pathway end-product, and valine, the product of a parallel pathway, serve as allosteric inhibitor and activator, respectively. This enzyme is thus a useful model system for studying the structural basis of allosteric control mechanisms. RESULTS We report the crystal structure of TD at 2.8 A resolution. The tetramer has 222 symmetry, with C-terminal regulatory domains projecting out from a core of catalytic PLP-containing N-terminal domains. The subunits, and especially the regulatory domains, associate extensively to form dimers, which associate less extensively to form the tetramer. Within the dimer, each monomer twists approximately 150 degrees around a thin neck between the domains to place its catalytic domain adjacent to the regulatory domain of the other subunit. CONCLUSIONS The structure of TD and its comparison with related structures and other data lead to the tentative identification of the regulatory binding site and revealed several implications for the allosteric mechanism. This work prepares the way for detailed structure/function studies of the complex allosteric behaviour of this enzyme.

The CCPN project: an interim report on a data model for the NMR community.

A recent workshop discusses the progress toward integrating NMR data into a unifying data model.

The PDB data uniformity project

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the data uniformity project that is underway to address the inconsistency in PDB data.

Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: Structure and glycosylase mechanism revisited†

The DNA repair enzyme uracil DNA glycosylase (UDG) catalyzes the hydrolysis of premutagenic uracil residues from single‐stranded or duplex DNA, producing free uracil and abasic DNA. Here we report the high‐resolution crystal structures of free UDG from Escherichia coli strain B (1.60 Å), its complex with uracil (1.50 Å), and a second active‐site complex with glycerol (1.43 Å). These represent the first high‐resolution structures of a prokaryotic UDG to be reported. The overall structure of the E. coli enzyme is more similar to the human UDG than the herpes virus enzyme. Significant differences between the bacterial and viral structures are seen in the side‐chain positions of the putative general‐acid (His187) and base (Asp64), similar to differences previously observed between the viral and human enzymes. In general, the active‐site loop that contains His187 appears preorganized in comparison with the viral and human enzymes, requiring smaller substrate‐induced conformational changes to bring active‐site groups into catalytic position. These structural differences may be related to the large differences in the mechanism of uracil recognition used by the E. coli and viral enzymes. The pH dependence of kcat for wild‐type UDG and the D64N and H187Q mutant enzymes is consistent with general‐base catalysis by Asp64, but provides no evidence for a general‐acid catalyst. The catalytic mechanism of UDG is critically discussed with respect to these results. Proteins 1999;35:13–24. 

Antibody modeling assessment.

A blinded study to assess the state of the art in three‐dimensional structure modeling of the variable region (Fv) of antibodies was conducted. Nine unpublished high‐resolution x‐ray Fab crystal structures covering a wide range of antigen‐binding site conformations were used as benchmark to compare Fv models generated by four structure prediction methodologies. The methodologies included two homology modeling strategies independently developed by CCG (Chemical Computer Group) and Accerlys Inc, and two fully automated antibody modeling servers: PIGS (Prediction of ImmunoGlobulin Structure), based on the canonical structure model, and Rosetta Antibody Modeling, based on homology modeling and Rosetta structure prediction methodology. The benchmark structure sequences were submitted to Accelrys and CCG and a set of models for each of the nine antibody structures were generated. PIGS and Rosetta models were obtained using the default parameters of the servers. In most cases, we found good agreement between the models and x‐ray structures. The average rmsd (root mean square deviation) values calculated over the backbone atoms between the models and structures were fairly consistent, around 1.2 Å. Average rmsd values of the framework and hypervariable loops with canonical structures (L1, L2, L3, H1, and H2) were close to 1.0 Å. H3 prediction yielded rmsd values around 3.0 Å for most of the models. Quality assessment of the models and the relative strengths and weaknesses of the methods are discussed. We hope this initiative will serve as a model of scientific partnership and look forward to future antibody modeling assessments. Proteins 2011;

A biological macromolecule crystallization database: A basis for a crystallization strategy

Abstract A crystallization database, the Biological Macromolecule Crystallization Database, containing crystal data and the crystallization conditions for more than 1000 crystal forms of over 600 biological macromolecules, has been compiled from the scientific literature. Data for proteins, protein: protein complexes, nucleic acids, nucleic-acid: nucleic-acid complexes, protein: nucleic-acid complexes and viruses have been included. The general information catalogued for each macromolecule. The crystal data molecular weight, the subunit composition, the presence of prosthetic group(s), and the source of the macromolecule. The crystal data include the unit cell parameters, space group, crystal density, crystal habit and size, and diffraction limit and lifetime. The crystallization data consist of the crystallization method, chemical additions to the crystal growth medium, macromolecule concentration, temperature, pH, and growth time. A result of the compilation of the crystallization data was the development of a general strategy for the crystallization of soluble proteins. The strategy employs vapor diffusion experiments with the most frequently used crystallization agents and microdialysis against low ionic strength to maximize the possiblity of obtaining crystals. A detailed outline of this strategy is presented.