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Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog
DOI:10.2210/pdb2oyq/pdb   NDB ID: PD0979
2OYQ
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 464590.15
    Molecule: Template DNA
    Polymer: 1 Type: dna Length: 21
    Chains: E, G, I, K
    Molecule: Primer DNA
    Polymer: 2 Type: dna Length: 15
    Chains: F, H, J, L
    Molecule: DNA polymerase
    Polymer: 3 Type: protein Length: 903
    Chains: A, B, C, D
    EC#: 2.7.7.7   
    Mutation: D222A, D327A
    Organism: Enterobacteria phage RB69
    Gene Name: 43
    UniProtKB: Protein Feature View | Search PDB | Q38087  
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

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  •   Source Hide
    Polymer: 1
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Enterobacteria phage rb69   Taxonomy   Expression System: Escherichia coli bl21(de3)  
     
  •   Related PDB Entries Hide
    Identifier Details
    1IG9   
    1RV2   
    2OZM   
    2OZS   
    2P5G   
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MG
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    MG Mg
    MAGNESIUM ION
    N5P
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    N5P C13 H17 N2 O14 P3
    1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]- BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO-1H- INDOLE
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    3DR
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    3DR C5 H11 O6 P dnaLinking
    N5I
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    N5I C13 H15 N2 O8 P dnaLinking
     
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  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: PD0979
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly 1       
Biological assembly 1 assigned by authors
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  •   Deposition Summary Hide
    Authors:   Zahn, K.E.,  Belrhali, H.,  Wallace, S.S.,  Doublie, S.

    Deposition:   2007-02-22
    Release:   2007-10-23
    Last Modified (REVDAT):   2009-02-24
     
  •   Revision History    Hide
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    2011-07-13
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  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.86
    R-Value: 0.234 (obs.)
    R-Free: 0.294
    Space Group: P 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 132.59 α = 90.00 
    b = 123.48 β = 96.22 
    c = 164.33 γ = 90.00