105M

SPERM WHALE MYOGLOBIN N-BUTYL ISOCYANIDE AT PH 9.0

• PDB DOI: https://doi.org/10.2210/pdb105M/pdb

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


• Deposited: 1997-12-18 Released: 1998-04-08 
• Deposition Author(s): Smith, R.D., Olson, J.S., Phillips Jr., G.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.268 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

Correlations between Bound N-Alkyl Isocyanide Orientations and Pathways for Ligand Binding in Recombinant Myoglobins

Smith, R.D.

(1999) Thesis 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.03 kDa 
• Atom Count: 1,386 
• Modelled 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 catodon	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	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NBN	D [auth A]	N-BUTYL ISOCYANIDE C5 H9 N FSBLVBBRXSCOKU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.268 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.72	α = 90
b = 30.061	β = 105.76
c = 35.191	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
XSCALE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-04-08 
Deposition Author(s): Smith, R.D., Olson, J.S., Phillips Jr., G.N.

Revision History  

• Version 1.0: 1998-04-08
  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: 2018-03-07
  Changes: Data collection, Other
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description