5LPC | pdb_00005lpc

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.

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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.

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

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 
• Modeled 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