2CMM

STRUCTURAL ANALYSIS OF THE MYOGLOBIN RECONSTITUTED WITH IRON PORPHINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of the myoglobin reconstituted with iron porphine.

Neya, S.Funasaki, N.Sato, T.Igarashi, N.Tanaka, N.

(1993) J.Biol.Chem. 268: 8935-8942


  • PubMed Abstract: 
  • Sperm whale apomyoglobin was complexed with iron porphine to examine the influence of completely removed heme side chains on the entire molecular structure. Paramagnetic NMR peak from the proximal histidine of the deoxy protein ensured formation of t ...

    Sperm whale apomyoglobin was complexed with iron porphine to examine the influence of completely removed heme side chains on the entire molecular structure. Paramagnetic NMR peak from the proximal histidine of the deoxy protein ensured formation of the iron-histidine bond. Porphine pyrrole-proton NMR signals of the cyanmet and deoxy derivatives are unusually sharp single lines manifesting rapid heme rotation about the iron-histidine bond. X-ray crystallographic structure of the cyanmet derivative, determined with a final R factor of 0.21 for 11,808 independent reflections ranging from 7 to 1.8 A, was resolved at 1.8 A resolution. The result confirmed 1:1 coupling between apomyoglobin and iron porphine. The cyano ligand adopts a bent configuration with an Fe-C-N angle of 127 degrees and a Fe-CN distance of 1.89 A. The overall globin structure and side chain conformations are remarkably similar to those of native myoglobin despite intensive disruption of the original heme-globin interactions. The native apoprotein structure unexpectedly conserved even after iron porphine insertion demonstrates that the complex polypeptide fold of holomyoglobin is more inherent in the amino acid sequence than is generally believed.


    Related Citations: 
    • The Crystal Structures of Cyanide Metmyoglobins Reconstituted with Iron(III) Complexes of Porphyrin, 5,10,15,20-Tetramethylporphyrin, and 5, 10,15,20-Tetraetylporphyrin
      Sato, T.,Tanaka, N.,Moriyama, H.,Matsumoto, O.,Takenaka, A.,Neya, S.,Funasaki, N.
      (1992) Bull.Chem.Soc.Jpn. 65: 739
    • Kinetic Studies on Co Binding to Reconstituted Myoglobins with Four Synthetic Hemes; Structural Control in Ligand Binding to Myoglobin
      Sato, T.,Tanaka, N.,Neya, S.,Funasaki, N.,Iizuka, T.,Shiro, Y.
      (1992) Biochim.Biophys.Acta 121: 1


    Organizational Affiliation

    Department of Physical Chemistry, Kyoto Pharmaceutical University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
153Physeter macrocephalusMutation(s): 0 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYN
Query on CYN

Download SDF File 
Download CCD File 
A
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
POR
Query on POR

Download SDF File 
Download CCD File 
A
PORPHYRIN FE(III)
C20 H12 Fe N4
XVFTZEQSXCJEIQ-MBVSZUDWBL
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.620α = 90.00
b = 76.230β = 90.00
c = 33.260γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance