1SCH | pdb_00001sch

PEANUT PEROXIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 
    0.262 (Depositor) 
  • R-Value Work: 
    0.199 (Depositor) 
  • R-Value Observed: 
    0.199 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

The crystal structure of peanut peroxidase.

Schuller, D.J.Ban, N.Huystee, R.B.McPherson, A.Poulos, T.L.

(1996) Structure 4: 311-321

  • DOI: https://doi.org/10.1016/s0969-2126(96)00035-4
  • Primary Citation Related Structures: 
    1SCH

  • PubMed Abstract: 

    Peroxidases catalyze a wide variety of peroxide-dependent oxidations. Based on sequence alignments, heme peroxidases have been divided into three classes. Crystal structures are available for peroxidases of classes I and II, but until now no structure has been determined for class III, the classical extracellular plant peroxidases. The crystal structure of peanut peroxidase has been solved to 2.7 A resolution. The helical fold is similar to that of known peroxidase structures. The 294-residue polypeptide chain is accompanied by a heme and two calcium ions, and there is some evidence of glycosylation. This is the first complete structure of a class III peroxidase and as such should serve as a model for other class III enzymes including the much-studied horseradish peroxidase. It may also aid in the interpretation of functional differences between the peroxidase classes. Ten helices conserved in class I and II peroxidases are also found in peanut peroxidase. Key residues of the heme environment and the location of two calcium ions are shared with class II peroxidases. Peanut peroxidase contains three unique helices, two of which contribute to the substrate access channel leading to the heme edge.


  • Organizational Affiliation
    • Department of Molecular Biology & Biochemistry, University of California, Irvine, CA 92717-3900, USA.

Macromolecule Content 

  • Total Structure Weight: 64.03 kDa 
  • Atom Count: 4,579 
  • Modeled Residue Count: 588 
  • Deposited Residue Count: 588 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PEANUT PEROXIDASE, MAJOR CATIONIC ISOZYME
A, B
294Arachis hypogaeaMutation(s): 0 
EC: 1.11.1.7
UniProt
Find proteins for P22195 (Arachis hypogaea)
Explore P22195 
Go to UniProtKB:  P22195
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22195
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free:  0.262 (Depositor) 
  • R-Value Work:  0.199 (Depositor) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.1α = 90
b = 97.2β = 90
c = 146.2γ = 90
Software Package:
Software NamePurpose
HOWARDdata collection
NIELSENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
NIELSENdata reduction
XUONG)data reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Derived calculations, Other, Polymer sequence
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Data collection, Database references, Structure summary