3RJJ Transferase, Lyase Dna date Apr 15, 2011
title Ternary Complex Crystal Structure Of Dna Polymerase Beta Wit 8odg Provides Insight Into Mutagenic Lesion Bypass
authors V.K.Batra, W.A.Beard, S.H.Wilson
compound source
Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7, 4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Tap56
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pwl11

Molecule: Dna (5'-D(Cpcpgpapcpgp(8og) Pcpgpcpaptpcpapgpc)-3');
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpc)-3')
Chain: P
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.202 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.480 79.410 54.910 90.00 105.51 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 8OG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceBinary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion., Batra VK, Shock DD, Beard WA, McKenna CE, Wilson SH, Proc Natl Acad Sci U S A. 2012 Jan 3;109(1):113-8. Epub 2011 Dec 16. PMID:22178760
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (3rjj.pdb1.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 3RJJ
  • CSU: Contacts of Structural Units for 3RJJ
  • Structure Factors (430 Kb)
  • Retrieve 3RJJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RJJ from S2C, [Save to disk]
  • Re-refined 3rjj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RJJ 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 3RJJ
  • 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 3RJJ, from MSDmotif at EBI
  • Fold representative 3rjj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rjj_A] [3rjj_P] [3rjj_T] [3rjj_D] [3rjj]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3RJJ: [HhH1] [POLXc ] by SMART
  • Other resources with information on 3RJJ
  • Community annotation for 3RJJ at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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