7MNH

V59W mutant of Dehaloperoxidase A from Amphitrite ornata treated with Fluoride

• PDB DOI: https://doi.org/10.2210/pdb7MNH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Amphitrite ornata
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-04-30 Released: 2021-11-24 
• Deposition Author(s): Shay, M.R., Thompson, M.K., Franzen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 0.187 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Starting Model: experimental

Literature

A new inhibition mechanism in the multifunctional catalytic hemoglobin dehaloperoxidase as revealed by the DHP A(V59W) mutant: A spectroscopic and crystallographic study

Thompson, M.K., Shay, M.R., Dumarieh, R., Ghiladi, R.A., Franzen, S.

(2021) J Porphyr Phthalocyanines 25: 756-771

• DOI: https://doi.org/10.1142/S1088424621500826

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.96 kDa 
• Atom Count: 2,725 
• Modelled Residue Count: 274 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehaloperoxidase A	A, B	138	Amphitrite ornata	Mutation(s): 1
UniProt
Find proteins for Q9NAV8 (Amphitrite ornata) Explore Q9NAV8  Go to UniProtKB:  Q9NAV8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 0.187 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.699	α = 90
b = 67.254	β = 90
c = 69.305	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Shay, M.R., Thompson, M.K., Franzen, S.

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description