2CMM | pdb_00002cmm

STRUCTURAL ANALYSIS OF THE MYOGLOBIN RECONSTITUTED WITH IRON PORPHINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 
    0.187 (Depositor) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 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 Biological Chem 268: 8935-8942

  • DOI: https://doi.org/10.2210/pdb2cmm/pdb
  • Primary Citation Related Structures: 
    2CMM

  • 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 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.


  • Organizational Affiliation
    • Department of Physical Chemistry, Kyoto Pharmaceutical University, Japan.

Macromolecule Content 

  • Total Structure Weight: 17.63 kDa 
  • Atom Count: 1,303 
  • Modeled Residue Count: 153 
  • Deposited Residue Count: 153 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MYOGLOBIN153Physeter macrocephalusMutation(s): 0 
EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POR

Query on POR



Download:Ideal Coordinates CCD File
C [auth A]PORPHYRIN FE(III)
C20 H12 Fe N4
XVFTZEQSXCJEIQ-QDJBTJTOSA-N
CYN

Query on CYN



Download:Ideal Coordinates CCD File
B [auth A]CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work:  0.187 (Depositor) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.62α = 90
b = 76.23β = 90
c = 33.26γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Other