3RJH Transferase, Lyase Dna date Apr 15, 2011
title Ternary Complex Of Dna Polymerase Beta With A Gapped Dna Con (Syn)8odg:Da At Primer Terminus And Dg:Dcmp(Cf2)Ppin The Ac
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(Gpcptpgpaptpgpcpgpa)-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 0.204 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.530 79.910 55.460 90.00 108.04 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand 6CF, 8OG, CL, MG, 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] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (3rjh.pdb1.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 3RJH
  • CSU: Contacts of Structural Units for 3RJH
  • Structure Factors (173 Kb)
  • Retrieve 3RJH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RJH from S2C, [Save to disk]
  • Re-refined 3rjh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RJH 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 3RJH
  • 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 3RJH, from MSDmotif at EBI
  • Fold representative 3rjh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rjh_A] [3rjh_D] [3rjh_P] [3rjh] [3rjh_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3RJH: [HhH1] [POLXc ] by SMART
  • Other resources with information on 3RJH
  • Community annotation for 3RJH at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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