4Z53

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

PDB DOI: https://doi.org/10.2210/pdb4Z53/pdb
NAKB: 4Z53

Classification: ISOMERASE
Organism(s): Streptococcus pneumoniae TIGR4, Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-04-02 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: 3.26 Å
R-Value Free: 0.207
R-Value Work: 0.173
R-Value Observed: 0.175

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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: 180.29 kDa
Atom Count: 11,084
Modelled Residue Count: 1,421
Deposited Residue Count: 1,520
Unique protein chains: 1
Unique nucleic acid chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A	A, B	742	Streptococcus pneumoniae TIGR4	Mutation(s): 2 Gene Names: parE, SP_0852, parC, SP_0855 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q59961 Go to UniProtKB: Q59961
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P72525 Go to UniProtKB: P72525
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q59961P72525
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
E-site DNA	C [auth E]	7	Escherichia coli
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
E-site DNA	D [auth F]	11	Escherichia coli
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
E-site DNA	E [auth G]	7	Escherichia coli
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
E-site DNA	F [auth H]	11	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TR6 Query on TR6 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]	Trovafloxacin C₂₀ H₁₅ F₃ N₄ O₃ WVPSKSLAZQPAKQ-CDMJZVDBSA-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 G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	G [auth A], H [auth A], I [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.26 Å
R-Value Free: 0.207
R-Value Work: 0.173
R-Value Observed: 0.175
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.83	α = 90
b = 157.83	β = 90
c = 210.58	γ = 120

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, Derived calculations, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary