2VWJ Dna Replication date Jun 25, 2008
title Uracil Recognition In Archaeal Dna Polymerases Captured By X-Ray Crystallography.
authors S.J.Firbank, J.Wardle, P.Heslop, R.J.Lewis, B.A.Connolly
compound source
Molecule: Dna Polymerase
Chain: A
Synonym: Tgo Polymerase Dna Complex, To Pol
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Thermococcus Gorgonarius
Organism_taxid: 71997
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Pet17b
Expression_system_plasmid: Pet

Molecule: 5'-D(Apapupgpgpapgpapcpgp Gpcptptptptpgpcpcpgptpgptpc)-3';
Chain: B

Synthetic: Yes
symmetry Space Group: I 2 2 2
R_factor 0.227 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.700 161.910 221.820 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.78 Å
ligand K enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity


  • Primary referenceUracil Recognition in Archaeal DNA Polymerases Captured by X-ray Crystallography., Firbank SJ, Wardle J, Heslop P, Lewis RJ, Connolly BA, J Mol Biol. 2008 Jun 7;. PMID:18614176
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (2vwj.pdb1.gz) 131 Kb
  • LPC: Ligand-Protein Contacts for 2VWJ
  • CSU: Contacts of Structural Units for 2VWJ
  • Likely Quarternary Molecular Structure file(s) for 2VWJ
  • Structure Factors (356 Kb)
  • Retrieve 2VWJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VWJ from S2C, [Save to disk]
  • Re-refined 2vwj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VWJ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2VWJ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2VWJ, from MSDmotif at EBI
  • Fold representative 2vwj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vwj_A] [2vwj] [2vwj_B]
  • SWISS-PROT database: [P56689]
  • Domain organization of [DPOL_THEGO] by SWISSPFAM
  • Domain found in 2VWJ: [POLBc ] by SMART
  • Other resources with information on 2VWJ
  • Community annotation for 2VWJ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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