3LPS | pdb_00003lps

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.253 (Depositor), 0.252 (DCC)
R-Value Work:
0.228 (Depositor), 0.228 (DCC)
R-Value Observed:
0.228 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of parE

Jung, H.Y., Heo, Y.-S.

To be published.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5GYJ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NOV Query on NOV Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NOVOBIOCIN C₃₁ H₃₆ N₂ O₁₁ YJQPYGGHQPGBLI-KGSXXDOSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.253 (Depositor), 0.252 (DCC)
R-Value Work: 0.228 (Depositor), 0.228 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-02-16

Deposition Author(s):

Revision History (Full details and data files)

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

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