3LPS

Crystal structure of parE

• PDB DOI: https://doi.org/10.2210/pdb3LPS/pdb

• Classification: ISOMERASE/ANTIBIOTIC
• Organism(s): Xanthomonas oryzae pv. oryzae KACC 10331
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-05 Released: 2011-02-16 
• Deposition Author(s): Jung, H.Y., Heo, Y.-S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Crystal structure of parE

Jung, H.Y., Heo, Y.-S.

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)

Macromolecule Content

• Total Structure Weight: 46.04 kDa 
• Atom Count: 2,948 
• Modelled Residue Count: 347 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Topoisomerase IV subunit B	A	408	Xanthomonas oryzae pv. oryzae KACC 10331	Mutation(s): 0  Gene Names: parE, XOO2969 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q5GYJ8 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)) Explore Q5GYJ8  Go to UniProtKB:  Q5GYJ8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NOV	B [auth A]	NOVOBIOCIN C31 H36 N2 O11 YJQPYGGHQPGBLI-KGSXXDOSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.12	α = 90
b = 105.12	β = 90
c = 135.969	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-16 
Deposition Author(s): Jung, H.Y., Heo, Y.-S.

Revision History  

• Version 1.0: 2011-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations