2XKK

CRYSTAL STRUCTURE OF MOXIFLOXACIN, DNA, and A. BAUMANNII TOPO IV (PARE-PARC FUSION TRUNCATE)

PDB DOI: https://doi.org/10.2210/pdb2XKK/pdb
NAKB: 2XKK

Classification: ISOMERASE/DNA/ANTIBIOTIC
Organism(s): Acinetobacter baumannii, synthetic construct
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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.270
R-Value Work: 0.194
R-Value Observed: 0.197

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1038/nsmb.1892
Primary Citation of 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.

Organizational Affiliation

Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK.

Macromolecule Content

Total Structure Weight: 194.15 kDa
Atom Count: 11,873
Modelled Residue Count: 1,455
Deposited Residue Count: 1,602
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TOPOISOMERASE IV	A, B [auth C]	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B0VP98
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA	C [auth E]	34	synthetic construct
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA	D [auth F]	34	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MFX Query on MFX Download Ideal Coordinates CCD File SDF format, chain I [auth E] SDF format, chain J [auth F] MOL2 format, chain I [auth E] MOL2 format, chain J [auth F] mmCIF format, chain I [auth E] mmCIF format, chain J [auth F]	I [auth E], J [auth F]	1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid C₂₁ H₂₄ F N₃ O₄ FABPRXSRWADJSP-MEDUHNTESA-N		Interactions Focus chain I [auth E] Focus chain J [auth F] Interactions & Density Focus chain I [auth E] Focus chain J [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth C] SDF format, chain H [auth C] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C] mmCIF format, chain F [auth A]	E [auth A], F [auth A], G [auth C], H [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth C] Focus chain H [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A, B [auth C]	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.270
R-Value Work: 0.194
R-Value Observed: 0.197
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.775	α = 90
b = 95.566	β = 108.27
c = 118.092	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-01
Type: Initial release
Version 1.1: 2011-10-12
Changes: Database references, Version format compliance
Version 1.2: 2023-12-20
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary