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 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

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 
• 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.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

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

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.4: 2024-11-13
  Changes: Structure summary