2XC9

BINARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE AND 1, N2-ETHENOGUANINE MODIFIED DNA, MAGNESIUM FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Metal Ion Dependence of the Active Site Conformation of the Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus Solfataricus

Irimia, A.Loukachevitch, L.V.Eoff, R.L.Guengerich, F.P.Egli, M.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1013

  • DOI: https://doi.org/10.1107/S1744309110029374
  • Primary Citation of Related Structures:  
    2XC9, 2XCA, 2XCP

  • PubMed Abstract: 

    Crystal structures of a binary Mg2+-form Dpo4-DNA complex with 1,N2-etheno-dG in the template strand as well as of ternary Mg2+-form Dpo4-DNA-dCTP/dGTP complexes with 8-oxoG in the template strand have been determined. Comparison of their conformations and active-site geometries with those of the corresponding Ca2+-form complexes revealed that the DNA and polymerase undergo subtle changes as a result of the catalytically more active Mg2+ occupying both the A and B sites.


  • Organizational Affiliation

    Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37232, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA POLYMERASE IV358Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: DPO4
EC: 2.7.7.7
UniProt
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97W02 
Go to UniProtKB:  Q97W02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97W02
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3'B [auth P]14synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*TP*CP*AP*CP*GNEP*GP*AP*AP*TP*CP*CP*TP*TP* CP*CP*CP*CP*C)-3'C [auth T]18synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.722α = 90
b = 102.125β = 90
c = 53.004γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references, Refinement description, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description