Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 185552.11 
• Atom Count: 11142 
• Residue Count: 1564 
• Unique protein chains: 2
• Unique nucleic acid chains: 4

3RAE

Quinolone(Levofloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae

• DOI: 10.2210/pdb3RAE/pdb
• NDB: NA1060

• Classification: ISOMERASE/DNA/ANTIBIOTIC
• Organism(s): Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
• Expression System: Escherichia coli


• Deposited: 2011-03-28 Released: 2012-04-25 
• Deposition Author(s): Laponogov, I., Pan, X.-S., Veselkov, D.A., McAuley, K.E., Fisher, L.M., Sanderson, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.226 
• R-Value Work: 0.186 

Literature

Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from Klebsiella pneumoniae and comparison with a related Streptococcus pneumoniae complex.

Veselkov, D.A., Laponogov, I., Pan, X.S., Selvarajah, J., Skamrova, G.B., Branstrom, A., Narasimhan, J., Prasad, J.V., Fisher, L.M., Sanderson, M.R.

(2016) Acta Crystallogr.,Sect.D 72: 488-496

• PubMed: 27050128 
• DOI: 10.1107/S2059798316001212
• Primary Citation of Related Structures:  
  5EIX


• PubMed Abstract: 
  

Klebsiella pneumoniae is a Gram-negative bacterium that is responsible for a range of common infections, including pulmonary pneumonia, bloodstream infections and meningitis. Certain strains of Klebsiella have become highly resistant to antibiotics. Despite the vast amount of research carried out on this class of bacteria, the molecular structure of its topoisomerase IV, a type II topoisomerase essential for catalysing chromosomal segregation, had remained unknown. In this paper, the structure of its DNA-cleavage complex is reported at 3.35 Å resolution. The complex is comprised of ParC breakage-reunion and ParE TOPRIM domains of K. pneumoniae topoisomerase IV with DNA stabilized by levofloxacin, a broad-spectrum fluoroquinolone antimicrobial agent. This complex is compared with a similar complex from Streptococcus pneumoniae, which has recently been solved.

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Organizational Affiliation: 

Randall Division of Cell and Molecular Biophysics, King's College London, 3rd Floor, New Hunt's House, Guy's Campus, London SE1 1UL, England.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA topoisomerase 4 subunit A	A, B	496	Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)	Mutation(s): 0  Gene Names: parC EC: 5.6.2.2
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Go to UniProtKB:  P72525

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
DNA topoisomerase 4 subunit B	C, D	268	Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)	Mutation(s): 0  Gene Names: parE EC: 5.6.2.2
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Go to UniProtKB:  Q59961

Entity ID: 3
Molecule	Chains	Length	Organism
5'-D(*CP*AP*TP*GP*AP*AP*T)-3'	E	7	N/A

Entity ID: 4
Molecule	Chains	Length	Organism
5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*G)-3'	F	11	N/A

Entity ID: 5
Molecule	Chains	Length	Organism
5'-D(*CP*GP*TP*GP*CP*AP*T)-3'	G	7	N/A

Entity ID: 6
Molecule	Chains	Length	Organism
5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*G)-3'	H	11	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A, B, C, D, G	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
LFX	F, H	(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 Levofloxacin C18 H20 F N3 O4 GSDSWSVVBLHKDQ-JTQLQIEISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.226 
• R-Value Work: 0.186 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 157.831	α = 90.00
b = 157.831	β = 90.00
c = 211.147	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	refinement
GDE	data collection
PHASER	phasing
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-28 
• Released Date: 2012-04-25 
• Deposition Author(s): Laponogov, I., Pan, X.-S., Veselkov, D.A., McAuley, K.E., Fisher, L.M., Sanderson, M.R.

Revision History 

• Version 1.0: 2012-04-25
  Type: Initial release
• Version 1.1: 2016-04-20
  Type: Database references