3RB0 Transferase Dna date Mar 28, 2011
title Dpo4 Extension Ternary Complex With 3'-Terminal Primer G Bas The 1-Methylguanine (M1g) Lesion
authors O.Rechkoblit, D.J.Patel
compound source
Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Ec: 2.7.7.7
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
Expression_system_plasmid: Pet28a

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

Synthetic: Yes
Other_details: Synthetic

Molecule: Dna (5'-D(Ccptpapapcp(Mg1) Pcptpapcpcpaptpcpcpapapcpc)-3');
Chain: E, J
Engineered: Yes
Other_details: Dna M1g-Modified Template Strand

Synthetic: Yes
Other_details: Synthetic
symmetry Space Group: P 1 21 1
R_factor 0.223 R_Free 0.294
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.421 110.362 102.268 90.00 101.28 90.00
method X-Ray Diffractionresolution 3.23 Å
ligand CA, DDG, DGT, MG1 enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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] (290 Kb) [Save to disk]
  • Biological Unit Coordinates (3rb0.pdb1.gz) 142 Kb
  • Biological Unit Coordinates (3rb0.pdb2.gz) 142 Kb
  • LPC: Ligand-Protein Contacts for 3RB0
  • CSU: Contacts of Structural Units for 3RB0
  • Structure Factors (149 Kb)
  • Retrieve 3RB0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RB0 from S2C, [Save to disk]
  • Re-refined 3rb0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RB0 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 3RB0
  • 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 3RB0, from MSDmotif at EBI
  • Fold representative 3rb0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rb0_D] [3rb0_A] [3rb0_J] [3rb0_B] [3rb0_E] [3rb0] [3rb0_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3RB0
  • Community annotation for 3RB0 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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