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RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (GC rich sequence)
DOI:10.2210/pdb3sq4/pdb   NDB ID: NA1208
3SQ4
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 114055.37
    Molecule: DNA polymerase
    Polymer: 1 Type: protein Length: 902
    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(P*CP*(2PR)P*TP*CP*GP*CP*CP*GP*CP*CP*GP*CP*GP*CP*GP*G)-3'
    Polymer: 2 Type: dna Length: 16
    Chains: T
    Details: template
    Molecule: 5'-D(*CP*GP*CP*GP*CP*GP*GP*CP*GP*GP*CP*GP*(2DA))-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
    3SQ2  RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence) 
    3SUN  RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite 2AP (AT rich sequence) 
    3SUO  RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite 2AP (GC rich sequence) 
    3SUP  RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite 2AP (GC rich sequence) 
    3SUQ  RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite 2AP (AT rich sequence) 
     
  •   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:3SQ4
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    2PR
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    2PR C10 H14 N5 O6 P DG dnaLinking
    2DA
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    2DA C10 H14 N5 O5 P DA dnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA1208
     
 
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:   2011-11-09
    Last Modified (REVDAT):   2011-11-30
     
  •   Revision History    Hide
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    2011-11-30
    Citation
    2011-11-16
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.23
    R-Value: 0.203 (obs.)
    R-Free: 0.238
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 74.68 α = 90.00 
    b = 120.47 β = 90.00 
    c = 130.99 γ = 90.00