9L8X | pdb_00009l8x

The crystal structure of Halogenases XhnO11 complex with vanadate

PDB DOI: https://doi.org/10.2210/pdb9L8X/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces xinghaiensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-28 Released: 2025-12-31
Deposition Author(s): Wu, L., Fang, S.Q., Nie, Q.Y., Tang, G.L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.247 (Depositor), 0.247 (DCC)
R-Value Work:
0.190 (Depositor), 0.192 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

The crystal structure of Halogenases XhnO11 complex with vanadate

Nie, Q.Y., Fang, S.Q., Wu, L., Tang, G.L.

To be published.

Macromolecule Content

Total Structure Weight: 116.46 kDa
Atom Count: 7,511
Modeled Residue Count: 916
Deposited Residue Count: 1,056
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vanadium-dependent haloperoxidase	A [auth B], B [auth A]	528	Streptomyces xinghaiensis	Mutation(s): 0 Gene Names: Sfr7A_13920, SFRA_005355
UniProt
Find proteins for A0A420V7T7 (Streptomyces xinghaiensis) Explore A0A420V7T7 Go to UniProtKB: A0A420V7T7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A420V7T7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VO4 (Subject of Investigation/LOI) Query on VO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain C [auth B] MOL2 format, chain E [auth A] MOL2 format, chain C [auth B] mmCIF format, chain E [auth A] mmCIF format, chain C [auth B]	C [auth B], E [auth A]	VANADATE ION O₄ V LSGOVYNHVSXFFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain E [auth A] Interactions & Density Focus chain C [auth B] Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.247 (Depositor), 0.247 (DCC)
R-Value Work: 0.190 (Depositor), 0.192 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.886	α = 90
b = 94.033	β = 90
c = 126.029	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-12-31
Type: Initial release

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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.