3FV5 | pdb_00003fv5

Crystal Structure of E. coli Topoisomerase IV co-complexed with inhibitor

PDB DOI: https://doi.org/10.2210/pdb3FV5/pdb

Classification: ISOMERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-15 Released: 2010-01-26
Deposition Author(s): Wei, Y., Charifson, P., LeTiran, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.240 (Depositor), 0.248 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Design and syntheses of novel C7-derived-aminobenzimidazole ureas: bacterial gyrase/topoisomerase IV inhibitors with potent Gram-positve antibacterial activity

Wei, Y., Letiran, A.

To be published.

Macromolecule Content

Total Structure Weight: 45.35 kDa
Atom Count: 3,325
Modeled Residue Count: 361
Deposited Residue Count: 402
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit B	A, B	201	Escherichia coli K-12	Mutation(s): 0 Gene Names: parE, nfxD, b3030, JW2998 EC: 5.99.1 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P20083 (Escherichia coli (strain K12)) Explore P20083 Go to UniProtKB: P20083
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20083
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1EU Query on 1EU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	1-(4-acetyl-6-pyridin-3-yl-1H-benzimidazol-2-yl)-3-ethylurea C₁₇ H₁₇ N₅ O₂ KDHATIBQZJAMKQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.240 (Depositor), 0.248 (DCC)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.199 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.42	α = 90
b = 72.84	β = 96.41
c = 70.97	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-01-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-01-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.