4Z2D

Quinolone(Levofloxacin)-DNA cleavage complex of gyrase from S. pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


This is version 1.2 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit AA,
C [auth B]
499Streptococcus pneumoniaeMutation(s): 0 
Gene Names: gyrABM52_0349
EC: 5.99.1.3
UniProt
Find proteins for Q8DPM2 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DPM2 
Go to UniProtKB:  Q8DPM2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DPM2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit BB [auth C],
D
269Streptococcus pneumoniaeMutation(s): 0 
Gene Names: gyrBBM52_1967DJ38_04430
EC: 5.99.1.3
UniProt
Find proteins for P0A4M0 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore P0A4M0 
Go to UniProtKB:  P0A4M0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A4M0
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
Symmetrized E-site DNAE,
H [auth G]
15Escherichia coli
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
Symmetrized E-site DNAF,
G [auth H]
19Escherichia coli
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.13α = 90
b = 95.88β = 90
c = 275.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description