Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18016.59 
• Atom Count: 1270 
• Residue Count: 153 
• Unique protein chains: 1

1MBI

X-RAY CRYSTAL STRUCTURE OF THE FERRIC SPERM WHALE MYOGLOBIN: IMIDAZOLE COMPLEX AT 2.0 ANGSTROMS RESOLUTION

• DOI: 10.2210/pdb1MBI/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Physeter catodon


• Deposited: 1990-06-25 Released: 1991-10-15 
• Deposition Author(s): Lionetti, C., Guanziroli, M.G., Frigerio, F., Ascenzi, P., Bolognesi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å

Literature

X-ray crystal structure of the ferric sperm whale myoglobin: imidazole complex at 2.0 A resolution.

Lionetti, C., Guanziroli, M.G., Frigerio, F., Ascenzi, P., Bolognesi, M.

(1991) J.Mol.Biol. 217: 409-412

• PubMed: 1994031 
• Primary Citation of Related Structures:  
  1SWM


• PubMed Abstract: 
  

The X-ray crystal structure of the ferric sperm whale (Physeter catodon) myoglobin:imidazole complex has been refined at 2.0 A resolution, to a final R-factor of 14.8%. The overall conformation of the protein is little affected by binding of the ligand. Imidazole is co-ordinated to the heme iron at the distal site, and forces distinguishable local changes in the surrounding protein residues. His64(E7) swings out of the distal pocket and becomes substantially exposed to the solvent: nevertheless, it stabilizes the exogenous ligand by hydrogen bonding. The side-chains of residues Arg45(CD3) and Asp60(E3) are also affected by imidazole association.

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Related Citations: 

• Reactivity of Ferric Aplysia and Sperm Whale Myoglobins Towards Imidazole. X-Ray and Binding Study
  Bolognesi, M.,Cannillo, E.,Ascenzi, P.,Giacometti, G.M.,Merli, A.,Brunori, M.
  (1982) J.Mol.Biol. 158: 305
• Aplysia Limacina Myoglobin. Crystallographic Analysis at 1.6 Angstroms Resolution
  Bolognesi, M.,Onesti, S.,Gatti, G.,Coda, A.,Ascenzi, P.,Brunori, M.
  (1989) J.Mol.Biol. 205: 529




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Organizational Affiliation: 

Dipartimento di Genetica e Microbiologia, Università di Pavia, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
MYOGLOBIN	A	153	Physeter catodon	Mutation(s): 0  Gene Names: MB
Find proteins for P02185 (Physeter catodon) Go to Gene View: MB Go to UniProtKB:  P02185

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
IMD	A	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 64.900	α = 90.00
b = 30.760	β = 105.67
c = 34.860	γ = 90.00

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1990-06-25 
• Released Date: 1991-10-15 
• Deposition Author(s): Lionetti, C., Guanziroli, M.G., Frigerio, F., Ascenzi, P., Bolognesi, M.

Revision History 

• Version 1.0: 1991-10-15
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance