Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) in complex with AP-site containing DNA substrate
DOI:10.2210/pdb2opf/pdb   NDB ID: PD0969
Primary Citation
  •   Molecular Description Hide
    Classification: Hydrolase/dna
    Structure Weight: 37554.79
    Molecule: 5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3'
    Polymer: 1 Type: dna Length: 12
    Chains: B
    Molecule: 5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
    Polymer: 2 Type: dna Length: 12
    Chains: C
    Molecule: Endonuclease VIII
    Polymer: 3 Type: protein Length: 262
    Chains: A
    Mutation: ALA:252, ARG:112, THR:34
    Organism: Escherichia coli
    Gene Names: nei b0714 JW0704
    UniProtKB: Search PDB | P50465   Protein Feature View
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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: Escherichia coli   Taxonomy   Expression System: Escherichia coli  
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    Identifier Details
  •   Ligand Chemical Component Hide
  •   Modified Residues Hide
    Identifier Formula Parent Type
    PED C5 H13 O6 P nonPolymer
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  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:PD0969
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors
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  •   Deposition Summary Hide
    Authors:   Golan, G.,  Zharov, D.O.,  Grollman, A.P.,  Shoham, G.

    Deposition:   2007-01-29
    Release:   2008-02-26
    Last Modified (REVDAT):   2011-07-13
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    Non-polymer description
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  •   Experimental Details Hide
    Exp. Data:
    Resolution[Å]:   1.85
    R-Value: 0.240 (obs.)
    R-Free: 0.267
    Space Group: P 43 2 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 73.56 α = 90.00 
    b = 73.56 β = 90.00 
    c = 170.11 γ = 90.00