3RMD 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
Ec: 2.7.7.7
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(Cpgptp(Ctg) Pgapaptpgpapcpapgpcpcpgpcpg)-3');
Chain: E, G, I, K
Engineered: Yes
Other_details: Dna Template

Synthetic: Yes

Molecule: Dna (5'-D(Gpcpgpgpcptpgptpcpaptptpcp 3');
Chain: F, H, J, L
Engineered: Yes
Other_details: Dna Primer

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.220 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
132.837 123.025 168.775 90.00 95.87 90.00
method X-Ray Diffractionresolution 2.98 Å
ligand CTG, DTP enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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] (648 Kb) [Save to disk]
  • Biological Unit Coordinates (3rmd.pdb1.gz) 164 Kb
  • Biological Unit Coordinates (3rmd.pdb2.gz) 169 Kb
  • Biological Unit Coordinates (3rmd.pdb3.gz) 168 Kb
  • Biological Unit Coordinates (3rmd.pdb4.gz) 165 Kb
  • LPC: Ligand-Protein Contacts for 3RMD
  • CSU: Contacts of Structural Units for 3RMD
  • Structure Factors (2295 Kb)
  • Retrieve 3RMD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RMD from S2C, [Save to disk]
  • Re-refined 3rmd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RMD 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 3RMD
  • 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 3RMD, from MSDmotif at EBI
  • Fold representative 3rmd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rmd] [3rmd_G] [3rmd_E] [3rmd_D] [3rmd_A] [3rmd_C] [3rmd_F] [3rmd_J] [3rmd_B] [3rmd_I] [3rmd_L] [3rmd_H] [3rmd_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3RMD: [POLBc ] by SMART
  • Other resources with information on 3RMD
  • Community annotation for 3RMD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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