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MutM (Fpg) bound to 5,6-dihydrouracil (DHU) containing DNA
DOI:10.2210/pdb1r2z/pdb   NDB ID: PD0474
1R2Z
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Hydrolase/dna
    Structure Weight: 38090.90
    Molecule: 5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'
    Polymer: 1 Type: dna Length: 12
    Chains: B
    Molecule: 5'-D(*TP*GP*CP*GP*TP*CP*CP*AP*(DHU)P*GP*TP*CP*TP*AP*CP*C)-3'
    Polymer: 2 Type: dna Length: 12
    Chains: C
    Molecule: MutM
    Polymer: 3 Type: protein Length: 274
    Chains: A
    EC#: 3.2.2.23   
    Mutation: E3Q
    Organism: Geobacillus stearothermophilus
    Gene Names: mutM fpg
    UniProtKB: Protein Feature View | Search PDB | P84131  
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Geobacillus stearothermophilus   Taxonomy   Expression System: Escherichia coli  
     
  •   Related PDB Entries Hide
    Identifier Details
    1L1T  Mutm (Fpg) Bound To Abasic-Site Containing DNA 
    1L1Z  Mutm (Fpg) Covalent-DNA Intermediate 
    1L2B  Mutm (Fpg) DNA End-Product Structure 
    1L2C  Mutm (Fpg)-DNA Estranged Thymine Mismatch Recognition Complex 
    1L2D  Mutm (Fpg)-DNA Estranged Guanine Mismatch Recognition Complex 
    1R2Y  MutM (Fpg) bound to 8-oxoguanine (oxoG) containing DNA 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    ZN
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    ZN Zn
    ZINC ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    UMP
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    UMP C9 H13 N2 O8 P nonPolymer
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: PD0474
     
 
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:   Fromme, J.C.,  Verdine, G.L.

    Deposition:   2003-09-30
    Release:   2003-10-14
    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]:   1.63
    R-Value: 0.208 (obs.)
    R-Free: 0.233
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 44.59 α = 90.00 
    b = 94.23 β = 90.00 
    c = 102.18 γ = 90.00