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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1EU	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.190 (DCC) 
• 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

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Wei, Y., Charifson, P., LeTiran, A.

Revision History  

• 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