4M3R

RB69 DNA polymerase ternary complex with dT/dG at position n-1 of primer/template duplex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant.

Xia, S., Konigsberg, W.H.

(2014) Protein Sci 23: 508-513

  • DOI: 10.1002/pro.2434
  • Primary Citation of Related Structures:  
    4M3R, 4M3T, 4M45, 4M3U, 4M3W, 4M3X, 4M3Y, 4M41, 4M42, 4M3Z

  • PubMed Abstract: 

    • Recent structures of DNA polymerase complexes with dGMPCPP/dT and dCTP/dA mispairs at the insertion site have shown that they adopt Watson-Crick geometry in the presence of Mn(2+) indicating that the tautomeric or ionization state of the base has cha ...

    Recent structures of DNA polymerase complexes with dGMPCPP/dT and dCTP/dA mispairs at the insertion site have shown that they adopt Watson-Crick geometry in the presence of Mn(2+) indicating that the tautomeric or ionization state of the base has changed. To see whether the tautomeric or ionization state of base-pair could be affected by its microenvironment, we determined 10 structures of an RB69 DNA polymerase quadruple mutant with dG/dT or dT/dG mispairs at position n-1 to n-5 of the Primer/Template duplex. Different shapes of the mispairs, including Watson-Crick geometry, have been observed, strongly suggesting that the local environment of base-pairs plays an important role in their tautomeric or ionization states.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520-8114.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseA903Escherichia phage RB69Mutation(s): 6 
Gene Names: 43
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for Q38087 (Escherichia phage RB69)
Explore Q38087 
Go to UniProtKB:  Q38087
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA templateT16N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA primerP13N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.07 Å
      • R-Value Free: 0.221 
      • R-Value Work: 0.178 
      • R-Value Observed: 0.180 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 78.371α = 90
      b = 119.391β = 90
      c = 129.956γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      AMoREphasing
      REFMACrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2014-02-12
        Type: Initial release
      • Version 1.1: 2014-04-09
        Changes: Database references