8VIX | pdb_00008vix

Hydrogen Peroxide-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera

PDB DOI: https://doi.org/10.2210/pdb8VIX/pdb
EM Map EMD-43270: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Corallina pilulifera
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-05 Released: 2025-01-15
Deposition Author(s): Hessefort, L.Z., Williams, D.R., Biegasiewicz, K.F.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.31 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8VIX

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

Literature

High-Resolution CryoEM unveils insights into the Catalytic Mechanism of a Vanadium-dependent Bromoperoxidase

Hessefort, L.Z., Williams, D.R., Biegasiewicz, K.F.

To be published.

Macromolecule Content

Total Structure Weight: 138.84 kDa
Atom Count: 9,146
Modeled Residue Count: 1,180
Deposited Residue Count: 1,268
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vanadium-dependent bromoperoxidase	A, B	634	Corallina pilulifera	Mutation(s): 0 EC: 1.11.1.18
UniProt
Find proteins for O81959 (Corallina pilulifera) Explore O81959 Go to UniProtKB: O81959
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O81959
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	VANADATE ION O₄ V LSGOVYNHVSXFFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
PER Query on PER Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], H [auth B], I [auth B]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.31 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1
MODEL REFINEMENT	Coot	0.9.8.7
RECONSTRUCTION	cryoSPARC	4.3.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Hessefort, L.Z.

Biegasiewicz, K.F.

Funding Organization	Location	Grant Number
Other government	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.