1HJT

SPERM WHALE MYOGLOBIN (FERROUS, NITRIC OXIDE BOUND)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.252 
  • R-Value Observed: 0.162 

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This is version 1.3 of the entry. See complete history


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

  • Primary Citation of 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MYOGLOBIN153Physeter catodonMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.252 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.453α = 90
b = 29.444β = 106.32
c = 35.328γ = 90
Software Package:
Software NamePurpose
SHELXL-96model building
X-PLORmodel building
SHELXL-96refinement
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
SHELXL-96phasing
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-11-12
    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: 2023-08-09
    Changes: Database references, Derived calculations, Other, Refinement description