3RMB Transferase Dna date Apr 20, 2011
title Crystal Structure Of A Replicative Dna Polymerase Bound To D Containing Thymine Glycol
authors P.Aller, S.Duclos, S.S.Wallace, S.Doublie
compound source
Molecule: Dna Polymerase
Chain: A, B, C, D
Synonym: Gp43
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage Rb69
Organism_taxid: 12353
Gene: 43, Gp43
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

Molecule: Dna (5'-D(Cpgpcp(Ctg) Pgpapaptpgpapcpapgpcpcpgpcpg)-3');
Chain: E, G, I, K
Engineered: Yes
Other_details: Dna Template

Synthetic: Yes

Molecule: Dna (5'-D(Gpcpgpgpcptpgptpcpaptptpcp
Chain: F, H, J, L
Engineered: Yes
Other_details: Dna Primer

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.224 R_Free 0.276
length a length b length c angle alpha angle beta angle gamma
133.528 123.439 164.291 90.00 96.84 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand CTG, SO4 enzyme Transferase E.C. BRENDA
A, D, C, B
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity

  • Primary referenceA Crystallographic Study of the Role of Sequence Context in Thymine Glycol Bypass by a Replicative DNA Polymerase Serendipitously Sheds Light on the Exonuclease Complex., Aller P, Duclos S, Wallace SS, Doublie S, J Mol Biol. 2011 Jul 18. PMID:21781974
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (653 Kb) [Save to disk]
  • Biological Unit Coordinates (3rmb.pdb1.gz) 169 Kb
  • Biological Unit Coordinates (3rmb.pdb2.gz) 169 Kb
  • Biological Unit Coordinates (3rmb.pdb3.gz) 170 Kb
  • Biological Unit Coordinates (3rmb.pdb4.gz) 162 Kb
  • LPC: Ligand-Protein Contacts for 3RMB
  • CSU: Contacts of Structural Units for 3RMB
  • Structure Factors (5145 Kb)
  • Retrieve 3RMB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RMB from S2C, [Save to disk]
  • Re-refined 3rmb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RMB 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 3RMB
  • 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 3RMB, from MSDmotif at EBI
  • Fold representative 3rmb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rmb_G] [3rmb_K] [3rmb_D] [3rmb_B] [3rmb_E] [3rmb_F] [3rmb_J] [3rmb_A] [3rmb_C] [3rmb_I] [3rmb_H] [3rmb] [3rmb_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3RMB: [POLBc ] by SMART
  • Other resources with information on 3RMB
  • Community annotation for 3RMB at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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