9H1M | pdb_00009h1m

Recombinant ferric horseradish peroxidase C1A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 
    0.189 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of ferric recombinant horseradish peroxidase.

Nesa, M.L.Mandal, S.K.Toelzer, C.Humer, D.Moody, P.C.E.Berger, I.Spadiut, O.Raven, E.L.

(2025) J Biol Inorg Chem 30: 221-227

  • DOI: https://doi.org/10.1007/s00775-025-02103-2
  • Primary Citation of Related Structures:  
    9H1M

  • PubMed Abstract: 

    Horseradish peroxidase (HRP), isolated from horseradish roots, is heavily glycosylated, making it difficult to crystallize. In this work, we produced recombinant HRP in E. coli and obtained an X-ray structure of the ferric enzyme at 1.63 Å resolution. The structure shows that the recombinant HRP contains four disulphide bonds and two calcium ions, which are highly conserved in class III peroxidase enzymes. The heme active site contains histidine residues at the proximal (His 170) and distal (His 42) positions, and an active site arginine (Arg 38). Surprisingly, an ethylene glycol molecule was identified in the active site, forming hydrogen bonds with His 42 and Arg 38 at the δ-heme edge. The high yields obtained from the recombinant expression system, and the successful crystallization of the enzyme pave the way for new structural studies in the future.


  • Organizational Affiliation
    • School of Chemistry, University of Bristol, Bristol, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxidase C1A309Armoracia rusticanaMutation(s): 0 
Gene Names: PRXC1AHPRC1
EC: 1.11.1.7
UniProt
Find proteins for P00433 (Armoracia rusticana)
Explore P00433 
Go to UniProtKB:  P00433
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00433
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
2HP
Query on 2HP

Download Ideal Coordinates CCD File 
G [auth A]DIHYDROGENPHOSPHATE ION
H2 O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-M
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth A],
I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free:  0.189 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.157α = 90
b = 67.061β = 90
c = 117.178γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
Cootmodel building
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Leverhulme TrustUnited Kingdom2024-263/4

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Database references