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Ring-Opening of the -OH-PdG Adduct in Ternary Complexes with the Sulfolobus solfataricus DNA polymerase Dpo4
DOI:10.2210/pdb4jv0/pdb   NDB ID: NA2306
4JV0
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 49357.07
    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*TP*(KAG)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*CP*C)-3')
    Polymer: 3 Type: dna Length: 14
    Chains: C
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   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   
    4JV1   
    4JV2   
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    CA
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    CA Ca
    CALCIUM ION
    DTP
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    DTP C10 H16 N5 O12 P3
    2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
    DTP:4JV0
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    KAG
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    KAG C14 H20 N5 O8 P G rnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA2306
     
 
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
     
  •   Revision History    Hide
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    2013-10-09
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.95
    R-Value: 0.200 (obs.)
    R-Free: 0.270
    Space Group: P 21 21 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 93.83 α = 90.00 
    b = 104.49 β = 90.00 
    c = 52.53 γ = 90.00