3RBE Transferase Dna date Mar 29, 2011
title Dpo4 Extension Ternary Complex With 3'-Terminal Primer T Bas The 3-Methylcytosine (M3c) Lesion
authors O.Rechkoblit, D.J.Patel
compound source
Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2
Gene: Dbh, Dpo4, Sso2448
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3) Ril Codon Plus
Expression_system_vector_type: Pet28a

Molecule: Dna (5'-D(Gptptpgpgpaptpgpgptpapgp(2
Chain: D, H
Engineered: Yes
Other_details: Dna Primer Strand (Dideoxy-Terminated At The

Synthetic: Yes
Other_details: Synthetic

Molecule: Dna (5'-D(Ccptpapapcp(Me6) Pcptpapcpcpaptpcpcpapapcpc)-3');
Chain: E, J
Engineered: Yes
Other_details: Dna M3c-Modified Template Strand

Synthetic: Yes
Other_details: Synthetic
symmetry Space Group: P 1 21 1
R_factor 0.226 R_Free 0.266
length a length b length c angle alpha angle beta angle gamma
52.904 109.860 101.291 90.00 100.99 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 2DT, CA, DGT, ME6 enzyme Transferase E.C. BRENDA
A, B

Primary referenceImplications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions., Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ, Structure. 2011 Jun 8;19(6):821-32. doi: 10.1016/j.str.2011.03.020. PMID:21645853
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (291 Kb) [Save to disk]
  • Biological Unit Coordinates (3rbe.pdb1.gz) 146 Kb
  • Biological Unit Coordinates (3rbe.pdb2.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 3RBE
  • CSU: Contacts of Structural Units for 3RBE
  • Structure Factors (200 Kb)
  • Retrieve 3RBE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RBE from S2C, [Save to disk]
  • Re-refined 3rbe structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RBE 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 3RBE
  • 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 3RBE, from MSDmotif at EBI
  • Fold representative 3rbe from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rbe_B] [3rbe_E] [3rbe_A] [3rbe_J] [3rbe] [3rbe_D] [3rbe_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3RBE
  • Community annotation for 3RBE at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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