1MBI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1016/0022-2836(91)90744-q
  • Primary Citation of 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 ...

    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.


    Related Citations: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MYOGLOBINA153Physeter catodonMutation(s): 0 
Gene Names: MB
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
D [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.9α = 90
b = 30.76β = 105.67
c = 34.86γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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