7ADX | pdb_00007adx

SFX structure of dehaloperoxidase B in the oxyferrous form

• PDB DOI: https://doi.org/10.2210/pdb7ADX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Amphitrite ornata
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-09-16 Released: 2021-10-06 
• Deposition Author(s): Moreno Chicano, T., Ebrahim, A., Worrall, J.W., Axford, D.A., Owada, S., Tosha, T., Sugimoto, H., Strange, R.W., Owen, R.L., Hough, M.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.191 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

SFX structure of dehaloperoxidase B from Amphitrite ornata in the oxyferrous form

Moreno Chicano, T., Ebrahim, A., Worrall, J.W., Axford, D.A., Owada, S., Tosha, T., Sugimoto, H., Strange, R.W., Owen, R.L., Hough, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.55 kDa 
• Atom Count: 2,307 
• Modeled Residue Count: 274 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehaloperoxidase B	A, B	138	Amphitrite ornata	Mutation(s): 0
UniProt
Find proteins for Q9NAV7 (Amphitrite ornata) Explore Q9NAV7  Go to UniProtKB:  Q9NAV7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
OXY	G [auth B]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.191 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.31	α = 90
b = 68.1	β = 90
c = 68.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Moreno Chicano, T., Ebrahim, A., Worrall, J.W., Axford, D.A., Owada, S., Tosha, T., Sugimoto, H., Strange, R.W., Owen, R.L., Hough, M.A.

---

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R021015/1

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description