1GZB

PEROXIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Pentacoordination of the heme iron of Arthromyces ramosus peroxidase shown by a 1.8 A resolution crystallographic study at pH 4.5.

Kunishima, N.Amada, F.Fukuyama, K.Kawamoto, M.Matsunaga, T.Matsubara, H.

(1996) FEBS Lett 378: 291-294

  • DOI: https://doi.org/10.1016/0014-5793(95)01458-6
  • Primary Citation of Related Structures:  
    1GZB

  • PubMed Abstract: 

    In the presence of ammonium sulfate the absorption spectra of a peroxidase from the fungus Arthromyces ramosus (ARP) showed that the low-spin component increased as the pH increased from 6.0 to 9.0, whereas in its absence ARP remained in the high-spin state in the pH range investigated. The crystal structure of ARP at pH 4.5 in the presence of ammonium sulfate at 1.8 A resolution showed that the electron density at the 6th position of the heme iron seen at pH 7.5 had disappeared and that the iron atom deviated markedly from the heme plane. These observations strongly suggest that under physiological conditions the heme of ARP is in the pentacoordinated high-spin state and that at a high pH the heme iron is able to bind ammonia, forming the low-spin state. The location of the water molecule at the distal side of the heme in peroxidases is also discussed.


  • Organizational Affiliation

    Department of Biology, Faculty of Science, Osaka University, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEROXIDASE344Agaricales sp. 'Arthromyces ramosusMutation(s): 0 
EC: 1.11.1.7
UniProt
Find proteins for P28313 (Arthromyces ramosus)
Explore P28313 
Go to UniProtKB:  P28313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28313
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
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: 1.80 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.57α = 90
b = 74.57β = 90
c = 117.47γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-03-12
    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 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary