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Selenium Derivatized RNA/DNA Hybrid in complex with RNase H Catalytic Domain D132N Mutant
DOI:10.2210/pdb3twh/pdb   NDB ID: NA1296
3TWH
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Hydrolase/rna/dna
    Structure Weight: 19885.15
    Molecule: Ribonuclease H
    Polymer: 1 Type: protein Length: 138
    Chains: A
    EC#: 3.1.26.4   
    Fragment: catalytic domain
    Mutation: D132N
    Organism: Bacillus halodurans
    Gene Names: rnhA BH0863
    UniProtKB: Protein Feature View | Search PDB | Q9KEI9  
    Molecule: RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')
    Polymer: 2 Type: rna Length: 6
    Chains: B
    Molecule: DNA (5'-D(*AP*TP*(SDG)P*TP*CP*(SDG))-3')
    Polymer: 3 Type: dna Length: 6
    Chains: C
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Bacillus halodurans   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
    1ZBI  BACILLUS HALODURANS RNASE H CATALYTIC DOMAIN MUTANT D132N IN COMPLEX WITH 12-MER RNA/DNA HYBRID 
    2G8U  B. HALODURANS RNASE H CATALYTIC DOMAIN D132N MUTANT IN COMPLEX WITH MG2+ AND RNA/DNA HYBRID 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MG
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    MG Mg
    MAGNESIUM ION
    PO4
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    PO4 O4 P
    PHOSPHATE ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    SDG
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    SDG C10 H14 N5 O6 P Se DG dnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA1296
     
 
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:   Rob, A.,  Gerlits, O.,  Jiang, J.S.,  Gan, J.H.,  Huang, Z.

    Deposition:   2011-09-21
    Release:   2012-10-03
    Last Modified (REVDAT):   2014-09-24
     
  •   Revision History    Hide
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    2014-09-24
    Citation
    2014-02-12
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   1.79
    R-Value: 0.177 (obs.)
    R-Free: 0.208
    Space Group: C 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 80.66 α = 90.00 
    b = 37.82 β = 96.60 
    c = 61.94 γ = 90.00