4Z4Q

Quinazolinedione(PD 0305970)-DNA cleavage complex of topoisomerase IV from S. pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae

Laponogov, I.Veselkov, D.A.Pan, X.-S.Selvarajah, J.Crevel, I.M.-T.Fisher, L.M.Sanderson, M.R.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit AA, B742Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: parESP_0852parCSP_0855
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q59961 
Go to UniProtKB:  Q59961
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P72525 
Go to UniProtKB:  P72525
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    V-site DNAC [auth E]7pBR322 based IG-lambda expression vector
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      V-site DNAD [auth F]11pBR322 based IG-lambda expression vector
      Protein Feature View
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      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        V-site DNAE [auth G]7pBR322 based IG-lambda expression vector
        Protein Feature View
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        • Reference Sequence
        • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 5
          MoleculeChainsLengthOrganismImage
          V-site DNAF [auth H]11pBR322 based IG-lambda expression vector
          Protein Feature View
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          • Reference Sequence
          Small Molecules
          Ligands 2 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          PDQ
          Query on PDQ

          Download Ideal Coordinates CCD File 
          K [auth F], L [auth H]3-amino-7-{(3R)-3-[(1S)-1-aminoethyl]pyrrolidin-1-yl}-1-cyclopropyl-6-fluoro-8-methylquinazoline-2,4(1H,3H)-dione
          C18 H24 F N5 O2
          SMONLCFJGCJROJ-WDEREUQCSA-N
           Ligand Interaction
          MG
          Query on MG

          Download Ideal Coordinates CCD File 
          G [auth A], H [auth A], I [auth B], J [auth B]MAGNESIUM ION
          Mg
          JLVVSXFLKOJNIY-UHFFFAOYSA-N
           Ligand Interaction
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 3.04 Å
          • R-Value Free: 0.205 
          • R-Value Work: 0.162 
          • R-Value Observed: 0.164 
          • Space Group: P 31 2 1
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 158.02α = 90
          b = 158.02β = 90
          c = 211.22γ = 120
          Software Package:
          Software NamePurpose
          PHENIXrefinement
          xia2data reduction
          xia2data scaling
          PHASERphasing

          Structure Validation

          View Full Validation Report



          Entry History & Funding Information

          Deposition Data


          Funding OrganizationLocationGrant Number
          Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K010069/1

          Revision History  (Full details and data files)

          • Version 1.0: 2016-09-14
            Type: Initial release
          • Version 1.1: 2017-08-30
            Changes: Author supporting evidence, Derived calculations