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Protein Data Bank (PDB)
The Protein Data Bank (PDB) serves as an archive for the 3D structures of biological macromolecules, established in 1971 by the RCSB. It contains detailed experimental data, including atomic coordinates and various structural factors, with over 162,000 structures available as of April 2020. Various data deposition and validation tools assist researchers in submitting and verifying structural data, ensuring accuracy and accessibility for scientific use.
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Protein Data Bank (PDB)
- 1. Protein Data Bank (PDB) AmandeepSingh Assistant Professor Department of Biotechnology GSSDGS Khalsa College Patiala
- 2. Introduction Experiments 3D structure of biological macromolecules Archive •Archive of experimentally determined 3D structures of biological macromolecules. • Established in 1971, by Research Collaboratory for Structural Bioinformatics (RCSB), Brookhaven National Laboratories, USA. • Archive contain atomic coordinates, bibliographic citations, primary and secondary structure information, crystallographic structure factors, NMR experimental data.
- 3. 43,186 Structures (1May, 2207) 162269 Structures (1 April 2020) PDB Archive X-Ray Diffraction NMR Neutron diffraction Cryo electron Microscopy Secondary Data Source of Primary Data Released data Un-released data
- 4. Harnessing data fromPDB X-Ray Diffraction NMR Neutron diffraction Cryo electron Microscopy Structure File mmCIF format PDB format PDBML/XML format 3 Formats Uncompressed File Compressed/Zip File (To reduce size)
- 5. Data Deposition Tools 1.Auto Dep Input Tool (ADIT) Helps in depositing structures to PDB. Structure Validation Database Submission Structural Coordinate Structure Factor File
- 6. Structure factor andCoordinate Electron distribution Coordinates of each atom Dots Intensity of X-Ray Phase of X-Ray Structure factor Electron Density Map
- 7. Data Deposition Tools 2.pdb_extract X-Ray Diffraction NMR Neutron diffraction Cryo electron Microscopy Structure File Statistical Information Assemble To reduce Manual labor
- 8. pdb_extract Files pdb_extract 2 mmCIFFiles macromolecular Crystallographic Information File File 1 File 2 Structural Factors Atomic Coordinates Structure determination statistics Serve as Input for PDB deposition
- 9. Data Deposition Tools 3.Ligand deposit Provide information about small molecules (ligands) bound to macromolecules Small molecules Large molecule Chemical Information Structural Information
- 10. Data Deposition Tools 4.Validation server Provide opportunity for checking format of coordinate file and Structure factor file. Structure Validation Database Submission Structural Coordinate Structure Factor File
- 11. Validation Structural Coordinate Structure Factor File PDB ormmCIF mmCIF or PDBML/XML Yes No Submitted Changes Submitted Yes No Submitted Changes Submitted Pre-Check Validation
- 12. 4. Validation server •It also check entries which should have Unit cell, space groups, chain IDs, TER card (at the end of each chain) • Time taken for validation depends upon the size of the structure. Final report Summary reportAtlas Entry Structural Information • Bond distance • Angle comparison • Torsion angle comparison • Base morphology • Molecular graphic images