2V1I

Crystal structure of radiation-induced metmyoglobin - aqua ferrous myoglobin at pH 6.8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic and Spectroscopic Studies of Peroxide-Derived Myoglobin Compound II and Occurrence of Protonated Fe(Iv)-O

Hersleth, H.-P.Uchida, T.Rohr, A.K.Teschner, T.Schunemann, V.Kitagawa, T.Trautwein, A.X.Gorbitz, C.H.Andersson, K.K.

(2007) J.Biol.Chem. 282: 23372

  • DOI: 10.1074/jbc.M701948200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • High resolution crystal structures of myoglobin in the pH range 5.2-8.7 have been used as models for the peroxide-derived compound II intermediates in heme peroxidases and oxygenases. The observed Fe-O bond length (1.86-1.90 A) is consistent with tha ...

    High resolution crystal structures of myoglobin in the pH range 5.2-8.7 have been used as models for the peroxide-derived compound II intermediates in heme peroxidases and oxygenases. The observed Fe-O bond length (1.86-1.90 A) is consistent with that of a single bond. The compound II state of myoglobin in crystals was controlled by single-crystal microspectrophotometry before and after synchrotron data collection. We observe some radiation-induced changes in both compound II (resulting in intermediate H) and in the resting ferric state of myoglobin. These radiation-induced states are quite unstable, and compound II and ferric myoglobin are immediately regenerated through a short heating above the glass transition temperature (<1 s) of the crystals. It is unclear how this influences our compound II structures compared with the unaffected compound II, but some crystallographic data suggest that the influence on the Fe-O bond distance is minimal. Based on our crystallographic and spectroscopic data we suggest that for myoglobin the compound II intermediate consists of an Fe(IV)-O species with a single bond. The presence of Fe(IV) is indicated by a small isomer shift of delta = 0.07 mm/s from Mössbauer spectroscopy. Earlier quantum refinements (crystallographic refinement where the molecular-mechanics potential is replaced by a quantum chemical calculation) and density functional theory calculations suggest that this intermediate H species is protonated.


    Organizational Affiliation

    Department of Chemistry, University of Oslo, PO Box 1033, Blindern, Oslo N-0315, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
153Equus caballusMutation(s): 0 
Gene Names: MB
Find proteins for P68082 (Equus caballus)
Go to Gene View: MB
Go to UniProtKB:  P68082
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.137 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.872α = 90.00
b = 28.762β = 106.13
c = 35.347γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2011-06-02
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance