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RB69 DNA Polymerase Ternary Complex with dUpCpp Opposite dA
DOI:10.2210/pdb3sq1/pdb   NDB ID: NA1206
3SQ1
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 114554.82
    Molecule: DNA polymerase
    Polymer: 1 Type: protein Length: 901
    Chains: A
    EC#: 2.7.7.7   
    Mutation: yes
    Organism: Enterobacteria phage RB69
    Gene Name: 43
    UniProtKB: Protein Feature View | Search PDB | Q38087  
    Molecule: 5'-D(*TP*CP*GP*AP*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
    Molecule: 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
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Enterobacteria phage rb69   Taxonomy   Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3SPY  RB69 DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA 
    3SPZ  RB69 DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA (Ca2+) 
    3SQ0  RB69 DNA Polymerase(L561A/S565G/Y567A) Ternary Complex with dUpNpp Opposite dA (Mn2+) 
    3SQ2  RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence) 
    3SQ4  RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (GC rich sequence) 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    CA
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    CA Ca
    CALCIUM ION
    DUP
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    DUP C9 H16 N3 O13 P3
    2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
    DUP:3SQ1
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    DOC
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    DOC C9 H14 N3 O6 P DC dnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA1206
     
 
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:   Xia, S.,  Konigsberg, W.H.,  Wang, J.

    Deposition:   2011-07-04
    Release:   2011-10-12
    Last Modified (REVDAT):   2011-11-02
     
  •   Revision History    Hide
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    2011-11-02
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   1.82
    R-Value: 0.184 (obs.)
    R-Free: 0.213
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 75.10 α = 90.00 
    b = 120.47 β = 90.00 
    c = 130.56 γ = 90.00