2XKJ | pdb_00002xkj

CRYSTAL STRUCTURE OF CATALYTIC CORE OF A. BAUMANNII TOPO IV (PARE- PARC FUSION TRUNCATE)

• PDB DOI: https://doi.org/10.2210/pdb2XKJ/pdb

• Classification: ISOMERASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-07-08 Released: 2010-09-01 
• Deposition Author(s): Wohlkonig, A., Chan, P.F., Fosberry, A.P., Homes, P., Huang, J., Kranz, M., Leydon, V.R., Miles, T.J., Pearson, N.D., Perera, R.L., Shillings, A.J., Gwynn, M.N., Bax, B.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.213 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Structural Basis of Quinolone Inhibition of Type Iia Topoisomerases and Target-Mediated Resistance

Wohlkonig, A., Chan, P.F., Fosberry, A.P., Homes, P., Huang, J., Kranz, M., Leydon, V.R., Miles, T.J., Pearson, N.D., Perera, R.L., Shillings, A.J., Gwynn, M.N., Bax, B.D.

(2010) Nat Struct Mol Biol 17: 1152

• PubMed: 20802486 
• DOI: https://doi.org/10.1038/nsmb.1892
• Primary Citation Related Structures: 
  2XKJ, 2XKK


• PubMed Abstract: 
  

  Quinolone antibacterials have been used to treat bacterial infections for over 40 years. A crystal structure of moxifloxacin in complex with Acinetobacter baumannii topoisomerase IV now shows the wedge-shaped quinolone stacking between base pairs at the DNA cleavage site and binding conserved residues in the DNA cleavage domain through chelation of a noncatalytic magnesium ion. This provides a molecular basis for the quinolone inhibition mechanism, resistance mutations and invariant quinolone antibacterial structural features.

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Organizational Affiliation: 
• Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 86.37 kDa 
• Atom Count: 6,323 
• Modeled Residue Count: 721 
• Deposited Residue Count: 767 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TOPOISOMERASE IV	A [auth E]	767	Acinetobacter baumannii	Mutation(s): 0  EC: 5.99.1 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for B0VP98 (Acinetobacter baumannii (strain SDF)) Explore B0VP98  Go to UniProtKB:  B0VP98

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth E], D [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.213 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.389	α = 90
b = 74.433	β = 107.96
c = 80.211	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Wohlkonig, A., Chan, P.F., Fosberry, A.P., Homes, P., Huang, J., Kranz, M., Leydon, V.R., Miles, T.J., Pearson, N.D., Perera, R.L., Shillings, A.J., Gwynn, M.N., Bax, B.D.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-05-19
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-09-25
  Changes: Data collection, Other
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description