The Protein Data Bank

Abstract

The Protein Data Bank is a computer-based archival file for macromolecular structures. The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. Text included in each data entry gives pertinent information for the structure at hand (e.g. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory. All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americas), Tokyo (Japan), and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo. In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (e.g. a-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures.The Protein Data Bank' [1,2] was established in 1971 as a computer-based archival file for macromolecular structures. The purpose of the Bank is to collect, standardize, and distribute atomic co-ordinates and other data from crystallographic studies. As the number of solved protein and nucleic-acid structures has grown to the point where some lo7 characters are necessary to represent the co-ordinate information currently held, the need for such a computer-readable file has become very clear, and demands for the Bank's services have increased accordingly. The Protein Data Bank is one of several data base activities in the field of crystallography, e.g. the Bibliographic

Crystal Structures of Staphylococcus epidermidis Mevalonate Diphosphate Decarboxylase Bound to Inhibitory Analogs Reveal New Insight into Substrate Binding and Catalysis

“…MDD structures were obtained from the PDB (31) and are as follows: S. cerevisiae (1FI4); S. pyogenes (2GS8); S. aureus (2HK2 and 2HK3); T. brucei (2HKE); H. sapiens (3DJ4); M. musculus (3F0N); L. pneumophila (3LTO). Representations of all structures were generated using PyMol (32).…”

Two Residues in the T-loop of GlnK Determine NifL-dependent Nitrogen Control of nif Gene Expression

“…The 164-bp EcoRI-SacII fragment of pTA49 was replaced by a 164-bp EcoRI-SacII fragment generated with the mutagenic BK3 oligonucleotide (5Ј-CGCGCCGCGGTACAGCTCG-GCATGGC-3Ј) and the reverse primer, generating pTA52 (glnB T43A). The 285-bp SacII-SacI fragment of pTA49 was replaced by the 285-bp SacII-SacI fragment generated with the universal M [13][14][15][16][17][18][19][20] primer and mutagenic oligonucleotides BK4 (5Ј-TGTACCGCGGCGCGGAGTAT-TCGGTGG-3Ј), BK5 (5Ј-TGTACCGCGGCGCGGAGTATATGGTGAA-TTTTC-3Ј), or BK6 (5Ј-TGTACCGCGGCGCGGAGTATTCGGTGAA-TTTTC-3Ј), generating pTA53 (glnB M52S), pTA54 (glnB D54N), and pTA55 (glnB D54N;M52S), respectively. The replacement of the 164-bp EcoRI-SacII fragment of pTA53, pTA54, or pTA55 with the 164-bp EcoRI-SacII fragment of pTA52 then generated pTA58 (M52S;T43A), pTA56 (D54N;T43A), and pTA57 (M52S;T43A;D54N), respectively.…”

“…GlnK-A superposition of the E. coli GlnB and GlnK structures in which the T-loops are not disordered (Protein Data Bank (PDB) (18) accession codes 2PII and 1GNK, respectively) shows a good agreement in the core regions, but their T-loop conformations differ greatly (Fig. 3).…”

In vitro and In vivo antimycobacterial, hepatoprotective and immunomodulatory activity of Euclea natalensis and its mode of action

“…To identify homologous sequences with known 3D structure, a BLASTP (proteinprotein Basic Local Alignment Search Tool) search was carried out against the protein data bank (PDB) (Altschul et al, 1990;Bernstein et al, 1977). It searches a database of available protein structures with sequences to identify homologous structure using a query protein sequence with no structure.…”