5LPC

Crystal structure of Vanadium-dependent Haloperoxidase from A. marina

PDB DOI: https://doi.org/10.2210/pdb5LPC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Acaryochloris marina
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-08-12 Released: 2016-08-24
Deposition Author(s): Frank, A., Groll, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.249
R-Value Work: 0.207
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Characterization of a Cyanobacterial Haloperoxidase and Evaluation of its Biocatalytic Halogenation Potential.

Frank, A., Seel, C.J., Groll, M., Gulder, T.

(2016) Chembiochem 17: 2028-2032

PubMed: 27542168 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201600417
Primary Citation of Related Structures:
5LPC

PubMed Abstract:
Vanadium-dependent haloperoxidases (VHPOs) are a class of halogenating enzymes found in fungi, lichen, algae, and bacteria. We report the cloning, purification, and characterization of a functional VHPO from the cyanobacterium Acaryochloris marina (AmVHPO), including its structure determination by X-ray crystallography. Compared to other VHPOs, the AmVHPO features a unique set of disulfide bonds that stabilize the dodecameric assembly of the protein. Easy access by high-yield recombinant expression, as well as resistance towards organic solvents and temperature, together with a distinct halogenation reactivity, make this enzyme a promising starting point for the development of biocatalytic transformations.

Organizational Affiliation

Department Chemie, Center for Integrated Protein Science at the Department Chemie and Catalysis Research Center (CRC), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany.

Macromolecule Content

Total Structure Weight: 73.16 kDa
Atom Count: 4,816
Modelled Residue Count: 624
Deposited Residue Count: 666
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vanadium-dependent bromoperoxidase	A	666	Acaryochloris marina	Mutation(s): 0 Gene Names: AM1_4975
UniProt
Find proteins for B0C4R0 (Acaryochloris marina (strain MBIC 11017)) Explore B0C4R0 Go to UniProtKB: B0C4R0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B0C4R0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.249
R-Value Work: 0.207
R-Value Observed: 0.209
Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 306.16	α = 90
b = 306.16	β = 90
c = 306.16	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-08-24

Deposition Author(s):

Frank, A.

Groll, M.

Revision History (Full details and data files)

Version 1.0: 2016-08-24
Type: Initial release
Version 1.1: 2016-08-31
Changes: Database references
Version 1.2: 2016-11-09
Changes: Database references
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Refinement description