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Structural databases
Structural databases like PDB, CSD, and CATH contain 3D structural information of proteins, small molecules, and macromolecules determined through techniques like X-ray crystallography and NMR spectroscopy. These databases provide bibliographic data, atomic coordinates, and other details for each entry. PDB contains protein structures, CSD contains organic and metal-organic structures, and CATH classifies protein domains hierarchically. Structural databases have wide applications in structure prediction, analysis, mining, comparison, classification, structure refinement, and database annotation.
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Introduction to structural databases like PDB, CSD, and CATH, their purpose in crystallography, and common information they hold.
Details about PDB, its functions, and management by wwPDB, containing 3D protein structures obtained via various techniques.
Description of PDB file format including records like HEADER, TITLE, COMPND, ATOM, and their informational significance.
An example of a PDB file format illustrating how structural information is presented in a structured manner.
Introduction to CATH focusing on protein classification, its levels, and their significance in understanding protein structures.
CATH database aims and features including structural classifications, domain submission, and detection programs for protein analysis.
Description of CSD as a resource for 3D structures of organic compounds, its maintenance, and contribution by researchers globally.
Discussion on different applications of structural databases such as prediction, analysis, mining, comparison, and classification.
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Structural databases
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- 2. INTRODUCTION: • Structural databasesare the essential tools for all crystallographic works. • They are used in the process of producing, solving ,refining and publishing the structure of a new material.
- 3. THE COMMON INFORMATIONFOUND IN THE STRUCTURAL DATABASE INCLUDE: • Bibliographic information- author name, journal reference. • The chemical compound name, formula and oxidation states of the element present. • Number of formula units per unit cell(contents) • Dimension and symmetry of the unit cell. • symmetry of the structure. • Atomic coordinates, occupancies and thermal parameters. • Any special features of the experiment to collect the diffraction data. • The structures in the database have been solved using X-ray, neutron and electron diffraction techniques on sample, computational modelling or by using NMR.
- 4. PDB:(PROTEIN DATABASES) • Proteindatabase contains the information about 3D structures of the proteins. • The structural information of the protein can be determined by X-ray crystallography or Nuclear magnetic resonance(NMR) spectroscopy methods. • The PDB is overseen by an organisation called World Wide Protein Data Bank,wwPDB. • It is available at • www.wwpdb.org • www.pdbe.org • www.pdbj.org • Each entry in the PDB is provided with a unique identification number called PDB ID.It is a 4 letter identification number which consists of both alpha numeric characters.
- 7. PDB FILE FORMAT: ThePDB file format is the standard file format for protein structure file. It describes how molecules are held together in 3-D Structure of a protein. • The file contain hundreds or thousands of lines called records. Each record provides a different set of information like • HEADER: This reocord contains file name, date of submission and the PDB ID of the molecule. • TITLE: This record contains the title of the PDB entry. • COMPND: This record includes the protein name. • SOURCE: This record contains the name of the organism in which the particular protein is obtained. • KEYWDS: This record contains the keywords that describes about the protein.
- 8. PDB FILE FORMAT: •EXPDTA: This record contains the method used for the protein structure experiment. • AUTHOR: This record contains the name of the contributors who put the data into the database. • REVDATA: This record contains the revision date of the data related to protein.(Date of modification) • JRNL: This record contains the journal details of the literature about the protein • REMARK: This record contains the remarks about the protein structure. • DBREF: This record contains the reference to the protein in the sequence databases.
- 9. PDB FILE FORMAT: •SEQRES: This record contains information about the amino acid sequence of protein. • HET: This record contains details about the non protein substances in the protein. • HETNAM: This record contain the compound name of the non protein substances. • HETSYN: This record contains the identical compound name for the non protein substances. • FORMUL: This record contain the chemical formula of the non protein substances. • HELIX: This record holds the recognition of helical substructures.
- 10. PDB FILE FORMAT: •LINK: This record holds the recognition of inter-residue bonds. • ATOM: This record contains the atomic coordinates for the structure. • HEATM: This record contains the atomic coordinate record for non protein substances. • CONECT: This record contains the details about the bonds involved in non protein atoms. • MASTER: This record contains the details about the number of REMARK records, HET records, HELIX records, CONECT records and SEQRES records, etc. • END: This record represent the end of the file. •
- 12. THE PDB FORMAT •123456789+123456789+123456789+123456789+123456789+123456789+123456789+123456789+ • HEADER RETINOIC-ACID TRANSPORT 28-SEP-94 1CBS 1CBS 2 • COMPND CELLULAR RETINOIC-ACID-BINDING PROTEIN TYPE II COMPLEXED 1CBS 3 • COMPND 2 WITH ALL-TRANS-RETINOIC ACID (THE PRESUMED PHYSIOLOGICAL 1CBS 4 • COMPND 3 LIGAND) 1CBS 5 • SOURCE HUMAN (HOMO SAPIENS) 1CBS 6 • SOURCE 2 EXPRESSION SYSTEM: (ESCHERICHIA COLI) BL21 (DE3) 1CBS 7 • SOURCE 3 PLASMID: PET-3A 1CBS 8 • SOURCE 4 GENE: HUMAN CRABP-II 1CBS 9 • AUTHOR G.J.KLEYWEGT,T.BERGFORS,T.A.JONES 1CBS 10 • REVDAT 1 26-JAN-95 1CBS 0 1CBS 11 • -------------------------------------------------------------------------------------------------------------------------------------------
- 13. CATH: • The CATHmeans Class, Architecture,Topology and homologouus super family database for proteins • It was created by Janet Thornton and colleagues at the university college London. • It is available at http://www.biochem.ucl.ac.uk/bsm/cath • http://www.cathdb.info • It is a protein classification tool
- 14. IT CONSISTS OFFOUR LEVELS • Class: It includes structural conformations of proteins and their contents(alpha, beta, alpha/beta, etc.) • Architecture: It describes the gross orientation of secondary structures. It also gives information about folding of polypeptide chains. • Topology: It deals with the structures formed due to different topological arrangement of secondary structures. It explains the super families of the proteins. • Homologous super family: It compares the sequence and structure of various proteins. It helps to trace the evolutionary relationship among the proteins.
- 16. CATH • The CATHaims to provide official releases of protein structures every 12 months • It is a free publicly available online resource. • The latest version of CATH contains 1,14,215 domains,2178 homologous superfamilies,1110 fold groups.
- 18. THE CATH SERVER •The CATH have recently set up a server which allows the user to submit the co-ordinates of the newly determined structure for automatic classification in CATH. • DOMAIN BOUNDARIES AND SEQUENCE COMPARISON • CATH contains a detective program which is good for identifying multidomain proteins. • The results from the detective are returned to the user in less than a minutes. • Identified domains are scanned against non identical representatives from CATH using a global sequence alignment method
- 19. CATH SERVER • Ifa sequence match 95% then the domain is identical to one in CATH. • If a sequence match less than 30% then the structures are compared with all the sequence families (s-level). • ASSESING STRUCTURAL SIMILARITY: • TOPSCAN compares the secondary strucutres in each fold family to identify the possible fold families to which the new structures belong. • Subsequently the fast version of structure comparison SSAP scans represetatives from all the families • Structural pairs having a ssap score more than 80 are possible homologues while the score with 70-80 don’t have no sequence or functional similiarity. • Finally the SSAP structural alignment is displayed using a graphical display package.
- 22. CSD • The cambridgestructural Database is both a repository and a validated resource for 3-D structural data of molecules containing carbon and hydrogen. • It is used to know about the structures of organic, metal-organic and organometallic molecules • The specific entries in the CSD are complementary to PDB and Inorganic crystal structure database. • The data in the CSD is typically obtained by X-ray crystallography and less frequently by neutron diffraction
- 23. CSD • The datain the CSD is submitted by crystallographers and chemists from all over the world. • The CSD is maintained by an incorporated company called Cambridge Crystallographic Data centre, CCDC • The CCDC are publicly available for download at the point of publication. • The CSD is updated with about 50,000 new structures each year and are freely available to support teaching and other activities • The CSD is available at • www.ccdc.cam.ac.uk • webcsd.ccdc.cam.ac.uk
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