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Detailed structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases
DOI:10.2210/pdb3k9f/pdb   NDB ID: NA0217
3K9F
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Isomerase/dna
    Structure Weight: 195341.12
    Molecule: DNA topoisomerase 4 subunit A
    Polymer: 1 Type: protein Length: 496
    Chains: A, B
    EC#: 5.99.1.3   
    Fragment: residues 1-488
    Organism: Streptococcus pneumoniae
    Gene Names: parC SP_0855
    UniProtKB: Protein Feature View | Search PDB | P72525  
    Molecule: DNA topoisomerase 4 subunit B
    Polymer: 2 Type: protein Length: 268
    Chains: C, D
    EC#: 5.99.1.3   
    Fragment: residues 404-647
    Organism: Streptococcus pneumoniae
    Gene Names: parE SP_0852
    UniProtKB: Protein Feature View | Search PDB | Q59961  
    Molecule: DNA (5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*T)-3')
    Polymer: 3 Type: dna Length: 15
    Chains: E
    Details: DNA E site
    Molecule: DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3')
    Polymer: 4 Type: dna Length: 19
    Chains: F
    Details: DNA E site
    Molecule: DNA (5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*T)-3')
    Polymer: 5 Type: dna Length: 15
    Chains: G
    Details: DNA E site
    Molecule: DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3')
    Polymer: 6 Type: dna Length: 19
    Chains: H
    Details: DNA E site
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Streptococcus pneumoniae   Taxonomy   Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Streptococcus pneumoniae   Taxonomy   Expression System: Escherichia coli  
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 4
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 5
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 6
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    2NOV  Crystal structure of ParC55 from S. pneumoniae 
    3FOE  Quinolone: clinafloxacin 
    3FOF  Quinolone: moxifloxacin 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    LFX
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    LFX C18 H20 F N3 O4
    (3S)-9-fluoro-3-methyl-10-(4-methylpiperazin- 1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4- ij]quinoline-6-carboxylic acid
    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: NA0217
     
 
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:   Laponogov, I.,  Pan, X.-S.,  Veselkov, D.A.,  Fisher, L.M.,  Sanderson, M.R.

    Deposition:   2009-10-15
    Release:   2009-10-27
    Last Modified (REVDAT):   2010-07-14
     
  •   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
    Resolution[Å]:   2.90
    R-Value: 0.187 (obs.)
    R-Free: 0.218
    Space Group: P 32
    Unit Cell:
      Length [Å] Angles [°]
    a = 122.41 α = 90.00 
    b = 122.41 β = 90.00 
    c = 178.29 γ = 120.00