2YLJ | pdb_00002ylj

Horse Radish Peroxidase, mutant S167Y

• PDB DOI: https://doi.org/10.2210/pdb2YLJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Armoracia rusticana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-06-02 Released: 2012-06-13 
• Deposition Author(s): Roe, S.M., Al-Fartusie, F.S., Smith, A.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.189 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Engineering and Characterisation of Novel Protein Covalent Linkages in Horseradish Peroxidase (Hrp): Effect on Structure and Function.

Al-Fartusie, F.S.

(null) Ph D Thesis 

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 34.58 kDa 
• Atom Count: 2,934 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXIDASE C1A	A	306	Armoracia rusticana	Mutation(s): 1  EC: 1.11.1.7
UniProt
Find proteins for P00433 (Armoracia rusticana) Explore P00433  Go to UniProtKB:  P00433

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.189 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.4	α = 90
b = 67.37	β = 90
c = 117.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Roe, S.M., Al-Fartusie, F.S., Smith, A.T.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.2: 2025-10-01
  Changes: Derived calculations, Structure summary