1SWM | pdb_00001swm

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

• PDB DOI: https://doi.org/10.2210/pdb1SWM/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Physeter macrocephalus
• Mutation(s): No 


• Deposited: 1992-03-03 Released: 1994-01-31 
• Deposition Author(s): Rizzi, M., Ascenzi, P., Coda, A., Brunori, M., Bolognesi, M.

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Experimental Data Snapshot

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

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 Biology 217: 409-412

• PubMed: 1994031 
• DOI: https://doi.org/10.1016/0022-2836(91)90744-q
• Primary Citation Related Structures: 
  1MBI, 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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Organizational Affiliation: 
• Dipartimento di Genetica e Microbiologia, Università di Pavia, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.99 kDa 
• Atom Count: 1,391 
• Modeled Residue Count: 153 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYOGLOBIN	A	153	Physeter macrocephalus	Mutation(s): 0  EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
AZI	B [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work:  0.153 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.48	α = 90
b = 30.91	β = 105.7
c = 34.88	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Rizzi, M., Ascenzi, P., Coda, A., Brunori, M., Bolognesi, M.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  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