1FCS

CRYSTAL STRUCTURE OF A DISTAL SITE DOUBLE MUTANT OF SPERM WHALE MYOGLOBIN AT 1.6 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1FCS/pdb

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


• Deposited: 1993-04-20 Released: 1993-10-31 
• Deposition Author(s): Rizzi, M., Bolognesi, M., Coda, A., Cutruzzola, F., Travaglini Allocatelli, C., Brancaccio, A., Brunori, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work: 
  0.190 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Crystal structure of a distal site double mutant of sperm whale myoglobin at 1.6 A resolution.

Rizzi, M., Bolognesi, M., Coda, A., Cutruzzola, F., Allocatelli, C.T., Brancaccio, A., Brunori, M.

(1993) FEBS Lett 320: 13-16

• PubMed: 8462669 
• DOI: https://doi.org/10.1016/0014-5793(93)81647-i
• Primary Citation of Related Structures:  
  1FCS


• PubMed Abstract: 
  

  The three-dimensional structure of sperm whale myoglobin His64(E7)-->Val,Thr67(E10)-->Arg double mutant has been studied by X-ray crystallography at 1.6 A resolution, and refined to a crystallographic R-factor of 0.197. The Arg67(E10) side chain is extended in the direction of the ligand binding site, and its NH1 atom is at a distance of 3.11 A from the NH1 atom of Arg45(CD3), which is also pointing towards the distal site. Both are kept in this position by hydrogen bonding and electrostatic interactions with a solvent sulfate ion, located amongst the two, on the protein surface. No liganded water molecule is present at the sixth coordination position of the Fe(III) heme.

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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: 18.19 kDa 
• Atom Count: 1,399 
• Modelled Residue Count: 154 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYOGLOBIN	A	154	Physeter macrocephalus	Mutation(s): 0  Gene Names: SYNTHETIC GENE EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 2 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	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work:  0.190 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.3	α = 90
b = 91.3	β = 90
c = 45.86	γ = 120

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Rizzi, M., Bolognesi, M., Coda, A., Cutruzzola, F., Travaglini Allocatelli, C., Brancaccio, A., Brunori, M.

Revision History  

• Version 1.0: 1993-10-31
  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: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other