RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dTTP Opposite dG
DOI:10.2210/pdb3nhg/pdb   NDB ID: NA0600
3NHG
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 114749.91
    Molecule: DNA polymerase
    Polymer: 1 Type: protein Length: 903
    Chains: A
    EC#: 2.7.7.7   
    Mutation: D222A, D327A, S565G, Y567A
    Organism: Enterobacteria phage RB69
    Gene Name: 43
    UniProtKB: Protein Feature View | Search PDB | Q38087  
    Molecule: DNA (5'-D(*TP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
    Polymer: 2 Type: dna Length: 18
    Chains: T
    Details: Template DNA strand
    Molecule: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')
    Polymer: 3 Type: dna Length: 13
    Chains: P
    Details: Primer DNA strand
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Enterobacteria phage rb69   Taxonomy   Common Name: Bacteriophage rb69 Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1IG9   Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase 
    3LZJ   RB69 DNA Polymerase (Y567A) ternary complex with dCTP Opposite 7,8-Dihydro-8-oxoguanine 
    3NCI   RB69 DNA Polymerase Ternary Complex with dCTP Opposite dG at 1.8 angstrom resolution 
    3NDK   RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG 
    3NE6   RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dCTP Opposite dG 
    3NGI   RB69 DNA Polymerase (Y567A) ternary complex with dTTP Opposite dG 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    CA
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    CA Ca
    CALCIUM ION
    TTP
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    TTP C10 H17 N2 O14 P3
    THYMIDINE-5'-TRIPHOSPHATE
    TTP:3NHG
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    DOC
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    DOC C9 H14 N3 O6 P DC dnaLinking
     
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  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:NA0600
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Wang, M.,  Wang, J.,  Konigsberg, W.H.

    Deposition:   2010-06-14
    Release:   2011-01-26
    Last Modified (REVDAT):   2011-03-02
     
  •   Revision History    Hide
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    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.50
    R-Value: 0.188 (obs.)
    R-Free: 0.244
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 75.05 α = 90.00 
    b = 120.00 β = 90.00 
    c = 130.38 γ = 90.00