1H5I | pdb_00001h5i

X-ray induced reduction of horseradish peroxidase C1A Compound III (56-67% dose)

• PDB DOI: https://doi.org/10.2210/pdb1H5I/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Armoracia rusticana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-05-22 Released: 2002-05-27 
• Deposition Author(s): Berglund, G.I., Carlsson, G.H., Hajdu, J., Smith, A.T., Szoke, H., Henriksen, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

The Catalytic Pathway of Horseradish Peroxidase at High Resolution

Berglund, G.I., Carlsson, G.H., Smith, A.T., Szoke, H., Henriksen, A., Hajdu, J.

(2002) Nature 417: 463

• PubMed: 12024218 
• DOI: https://doi.org/10.1038/417463a
• Primary Citation Related Structures: 
  1H55, 1H57, 1H58, 1H5A, 1H5C, 1H5D, 1H5E, 1H5F, 1H5G, 1H5H, 1H5I, 1H5J, 1H5K, 1H5L, 1H5M, 1HCH


• PubMed Abstract: 
  

  A molecular description of oxygen and peroxide activation in biological systems is difficult, because electrons liberated during X-ray data collection reduce the active centres of redox enzymes catalysing these reactions. Here we describe an effective strategy to obtain crystal structures for high-valency redox intermediates and present a three-dimensional movie of the X-ray-driven catalytic reduction of a bound dioxygen species in horseradish peroxidase (HRP). We also describe separate experiments in which high-resolution structures could be obtained for all five oxidation states of HRP, showing such structures with preserved redox states for the first time.

---

Organizational Affiliation: 
• Department of Biochemistry, Uppsala University, Biomedical Center, Box 576, S-751 23 Uppsala, Sweden.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 34.84 kDa 
• Atom Count: 2,889 
• Modeled Residue Count: 306 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXIDASE C1A	A	308	Armoracia rusticana	Mutation(s): 0  EC: 1.11.1.7
UniProt
Find proteins for P00433 (Armoracia rusticana) Explore P00433  Go to UniProtKB:  P00433

Small Molecules

Ligands 4 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	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
PEO	F [auth A], G [auth A], H [auth A], I [auth A]	HYDROGEN PEROXIDE H2 O2 MHAJPDPJQMAIIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.318	α = 90
b = 67.392	β = 90
c = 117.467	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-27 
Deposition Author(s): Berglund, G.I., Carlsson, G.H., Hajdu, J., Smith, A.T., Szoke, H., Henriksen, A.

Revision History  

• Version 1.0: 2002-05-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary