4Z2D | pdb_00004z2d

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

PDB DOI: https://doi.org/10.2210/pdb4Z2D/pdb
NAKB: 4Z2D

Classification: ISOMERASE
Organism(s): Streptococcus pneumoniae, Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-03-29 Released: 2016-09-14
Deposition Author(s): Laponogov, I., Veselkov, D.A., Pan, X.-S., Selvarajah, J., Crevel, I.M.-T., Fisher, L.M., Sanderson, M.R.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.38 Å
R-Value Free:
0.280 (Depositor), 0.280 (DCC)
R-Value Work:
0.229 (Depositor), 0.230 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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.

Macromolecule Content

Total Structure Weight: 195.66 kDa
Atom Count: 10,118
Modelled Residue Count: 1,384
Deposited Residue Count: 1,604
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit A	A, C [auth B]	499	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: gyrA, BM52_0349 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q8DPM2 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DPM2 Go to UniProtKB: Q8DPM2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DPM2
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	B [auth C], D	269	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: gyrB, BM52_1967, DJ38_04430 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0A4M0 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore P0A4M0 Go to UniProtKB: P0A4M0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A4M0
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Symmetrized E-site DNA	E, H [auth G]	15	Escherichia coli
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Symmetrized E-site DNA	F, G [auth H]	19	Escherichia coli
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LFX Query on LFX Download Ideal Coordinates CCD File SDF format, chain K [auth F] SDF format, chain L [auth H] MOL2 format, chain K [auth F] MOL2 format, chain L [auth H] mmCIF format, chain K [auth F] mmCIF format, chain L [auth H]	K [auth F], L [auth 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 C₁₈ H₂₀ F N₃ O₄ GSDSWSVVBLHKDQ-JTQLQIEISA-N		Interactions Focus chain K [auth F] Focus chain L [auth H] Interactions & Density Focus chain K [auth F] Focus chain L [auth H]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth E] Focus chain J [auth F] Interactions & Density Focus chain I [auth E] Focus chain J [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.38 Å
R-Value Free: 0.280 (Depositor), 0.280 (DCC)
R-Value Work: 0.229 (Depositor), 0.230 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.13	α = 90
b = 95.88	β = 90
c = 275.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/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