7CMP | pdb_00007cmp

parE in complex with AMPPNP

PDB DOI: https://doi.org/10.2210/pdb7CMP/pdb

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

Deposited: 2020-07-28 Released: 2021-08-04
Deposition Author(s): Jung, H.Y., Heo, Y.-S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.260 (Depositor), 0.258 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of parE in complex with AMPPNP

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

To be published.

Macromolecule Content

Total Structure Weight: 183.84 kDa
Atom Count: 11,878
Modeled Residue Count: 1,496
Deposited Residue Count: 1,632
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit B	A, B, C, D	408	Xanthomonas oryzae pv. oryzae KACC 10331	Mutation(s): 0 Gene Names: parE, XOO2969 EC: 5.6.2.2
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.260 (Depositor), 0.258 (DCC)
R-Value Work: 0.202 (Depositor), 0.202 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.016	α = 90
b = 126.747	β = 109.61
c = 96.044	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-08-04

Deposition Author(s):

Jung, H.Y.

Heo, Y.-S.

Revision History (Full details and data files)

Version 1.0: 2021-08-04
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-09-17
Changes: Advisory, Derived calculations, Structure summary

7CMP | pdb_00007cmp

parE in complex with AMPPNP

Literature

Crystal structure of parE in complex with AMPPNP

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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