Ternary complex of gamma-OHPDG adduct modified dna with dna (-1 primer) polymerase iv and incoming dgtp
DOI:10.2210/pdb4jv1/pdb   NDB ID: NA2305
4JV1
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 49235.16
    Molecule: DNA polymerase IV
    Polymer: 1 Type: protein Length: 347
    Chains: A
    EC#: 2.7.7.7   
    Organism: Sulfolobus solfataricus P2
    Gene Names: dbh dpo4 SSO2448
    UniProtKB: Protein Feature View | Search PDB | Q97W02  
    Molecule: DNA (5'-D(P*CP*(HN1)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
    Polymer: 2 Type: dna Length: 15
    Chains: B
    Molecule: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3')
    Polymer: 3 Type: dna Length: 13
    Chains: C
     
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  •   Source Hide
    Polymer: 1
    Scientific Name: Sulfolobus solfataricus   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
    4JUZ    
    4JV0    
    4JV2    
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    CA
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    CA Ca
    CALCIUM ION
    DGT
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    DGT C10 H16 N5 O13 P3
    2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
    DGT:4JV1
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    HN1
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    HN1 C19 H30 N5 O9 P DG dnaLinking
     
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  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:NA2305
     
 
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:   Banerjee, S.,  Shanmugam, G.,  Stone, M.P.

    Deposition:   2013-03-25
    Release:   2013-08-28
    Last Modified (REVDAT):   2013-10-09
     
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    2013-10-09
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.30
    R-Value: 0.218 (obs.)
    R-Free: 0.269
    Space Group: P 21 21 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 93.27 α = 90.00 
    b = 102.18 β = 90.00 
    c = 52.73 γ = 90.00