1JDO | pdb_00001jdo

SPERM WHALE MYOGLOBIN (FERROUS, NITRIC OXIDE BOUND)

• PDB DOI: https://doi.org/10.2210/pdb1JDO/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Physeter macrocephalus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-02-10 Released: 1998-05-27 
• Deposition Author(s): Brucker, E.A., Phillips Jr., G.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.206 (Depositor) 
• R-Value Work: 
  0.142 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Nitric oxide myoglobin: crystal structure and analysis of ligand geometry.

Brucker, E.A., Olson, J.S., Ikeda-Saito, M., Phillips Jr., G.N.

(1998) Proteins 30: 352-356

• PubMed: 9533619 
• Primary Citation Related Structures: 
  1HJT, 1JDO


• PubMed Abstract: 
  

  The structure of the ferrous nitric oxide form of native sperm whale myoglobin has been determined by X-ray crystallography to 1.7 angstroms resolution. The nitric oxide ligand is bent with respect to the heme plane: the Fe-N-O angle is 112 degrees. This angle is smaller than those observed in model compounds and in lupin leghemoglobin. The exact angle appears to be influenced by the strength of the proximal bond and hydrogen bonding interactions between the distal histidine and the bound ligand. Specifically, the N(epsilon) atom of histidine64 is located 2.8 angstroms away from the nitrogen atom of the bound ligand, implying electrostatic stabilization of the FeNO complex. This interpretation is supported by mutagenesis studies. When histidine64 is replaced with apolar amino acids, the rate of nitric oxide dissociation from myoglobin increases tenfold.

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Organizational Affiliation: 
• Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005-1892, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.14 kDa 
• Atom Count: 1,416 
• Modeled 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): 2  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
NO	D [auth A]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.206 (Depositor) 
• R-Value Work:  0.142 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.506	α = 90
b = 91.506	β = 90
c = 45.853	γ = 120

Software Package:

Software Name	Purpose
SHELXL-96	model building
X-PLOR	model building
SHELXL-96	refinement
X-PLOR	refinement
XDS	data reduction
XSCALE	data scaling
SHELXL-96	phasing
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-05-27 
Deposition Author(s): Brucker, E.A., Phillips Jr., G.N.

Revision History  

• Version 1.0: 1998-05-27
  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: 2021-11-03
  Changes: Database references, Derived calculations, Other
• Version 1.4: 2023-08-09
  Changes: Refinement description
• Version 1.5: 2024-05-22
  Changes: Data collection