1H57

Structure of horseradish peroxidase C1A compound III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/417463a
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEROXIDASE C1A308Armoracia rusticanaMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

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C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

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D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
PEO
Query on PEO

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G [auth A],
H [auth A],
I [auth A]
HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
OXY
Query on OXY

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F [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.34α = 90
b = 67.227β = 90
c = 117.552γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-17
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references, Non-polymer description, Other, Version format compliance