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Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide
DOI:10.2210/pdb1jx4/pdb   NDB ID: PD0251
1JX4
Primary Citation
 
 
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  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 50458.52
    Molecule: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3'
    Polymer: 1 Type: dna Length: 13
    Chains: P
    Molecule: 5'-D(*T*TP*CP*AP*TP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
    Polymer: 2 Type: dna Length: 18
    Chains: T
    Molecule: DNA polymerase IV (family Y)
    Polymer: 3 Type: protein Length: 352
    Chains: A
    EC#: 2.7.7.7   
    Organism Sulfolobus solfataricus
    Gene Names dbh dpo4 SSO2448
    UniProtKB:   Protein Feature View | Search PDB | Q97W02  
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Sulfolobus solfataricus   Taxonomy   Expression System: Escherichia coli  
     
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    Identifier Details
    1JXL  the same protein complexed with different substrates 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name Interactions
    ADI
    Search 
    Download      		ADI C10 H15 N5 O8 P2
    2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE
    		ADI:1JX4
    CA
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    Download      		CA Ca
    CALCIUM ION
    MG
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    Download      		MG Mg
    MAGNESIUM ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    MSE
    Search      		MSE C5 H11 N O2 Se MET lPeptideLinking
     
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  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: PD0251
     
 
Data in orange boxes are gathered from external resources (when available).
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  •   Deposition Summary Hide
    Authors:   Ling, H.,  Boudsocq, F.,  Woodgate, R.,  Yang, W.

    Deposition:   2001-09-05
    Release:   2001-10-05
    Last Modified (REVDAT):   2011-11-16
     
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    2011-11-16
    Atom occupancy
    2011-07-13
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  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   1.70
    R-Value: 0.213 (obs.)
    R-Free: 0.228
    Space Group: P 21 21 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 97.09 α = 90.00 
    b = 102.82 β = 90.00 
    c = 52.30 γ = 90.00