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Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA
DOI:10.2210/pdb4mde/pdb   NDB ID: NA2693
4MDE
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 42852.04
    Molecule: Metallophosphoesterase
    Polymer: 1 Type: protein Length: 171
    Chains: A, B
    Mutation: D38N, L137M
    Organism: Ruminiclostridium thermocellum ATCC 27405
    Gene Name: Cthe_2768
    UniProtKB: Protein Feature View | Search PDB | A3DJ38  
    Molecule: DNA (5'-D(P*CP*CP*TP*GP*T)-3')
    Polymer: 2 Type: dna Length: 5
    Chains: C, D
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Clostridium thermocellum   Taxonomy   Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    4GP6   
    4GP7   
    4JST   
    4JSY   
    4JT2   
    4JT4   
    4MDF   
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    GDP
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    GDP C10 H15 N5 O11 P2
    GUANOSINE-5'-DIPHOSPHATE
    GDP:4MDE
    MG
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    MG Mg
    MAGNESIUM ION
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA2693
     
 
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:   Shuman, S.,  Das, U.,  Wang, L.K.,  Smith, P.,  Jacewicz, A.

    Deposition:   2013-08-22
    Release:   2013-11-06
    Last Modified (REVDAT):   2014-02-12
     
  •   Revision History    Hide
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    2014-02-12
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   1.80
    R-Value: 0.168 (obs.)
    R-Free: 0.206
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 54.44 α = 90.00 
    b = 73.12 β = 90.00 
    c = 119.04 γ = 90.00