Experimental Data Snapshot

  • Resolution: 1.7 Å
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history


A myoglobin variant with a polar substitution in a conserved hydrophobic cluster in the heme binding pocket.

Maurus, R.Overall, C.M.Bogumil, R.Luo, Y.Mauk, A.G.Smith, M.Brayer, G.D.

(1997) Biochim.Biophys.Acta 1341: 1-13

  • Primary Citation of Related Structures:  
  • Also Cited By: 1DWT, 1DWS, 1DWR, 1GJN

  • PubMed Abstract: 
  • Well-ordered internal amino acids can contribute significantly to the stability of proteins. To investigate the importance of the hydrophobic packing interface between helices G and H in the proximal heme pocket of horse heart myoglobin, the highly c ...

    Well-ordered internal amino acids can contribute significantly to the stability of proteins. To investigate the importance of the hydrophobic packing interface between helices G and H in the proximal heme pocket of horse heart myoglobin, the highly conserved amino acid, Leu104, was substituted with asparagine, a polar amino acid of similar size. The Leu104Asn mutant protein and its recombinant wild-type horse heart myoglobin counterpart were expressed from synthetic genes in Escherichia coli. Thermal denaturation of these two recombinant myoglobins, as studied by measurement of circular dichroism ellipticity at 222 nm, revealed that the Leu104Asn mutant had a significantly lower t(m) (71.8 +/- 1 degree C, pH 7.0) than recombinant wild-type myoglobin (81.3 +/- 1 degree C, pH 7.0). To examine the extent to which this 10 degrees C decrease in thermal stability was associated with structural perturbations, X-ray diffraction techniques were used to determine the three-dimensional structures of both the recombinant wild-type and Leu104Asn myoglobins to 0.17 nm resolution. Refinement of these structures gave final crystallographic R-factors of 16.0% and 17.9%, respectively. Structural comparison of the natural and recombinant wild-type myoglobins, together with absorption spectroscopic and electron paramagnetic resonance (EPR) analyses, confirmed the proper expression and folding of the recombinant protein in E. coli. Surprisingly, despite the decreased thermal stability of the Leu104Asn mutant, there are no significant structural differences between the mutant and wild-type myoglobins. EPR and absorption spectroscopic analyses further confirmed the similar nature of the heme iron centres in both proteins. Thus, the introduction of an energetically unfavourable change in side chain polarity at position 104 into a hydrophobic environment that does not support the hydrogen bonding potential of the mutant asparagine appears to perturb important stabilizing helix-helix and heme-protein interactions. The induced structural destabilization is thereby reflected by a significant decrease in the t(m) of horse heart myoglobin.

    Related Citations: 
    • High-Resolution Study of the Three-Dimensional Structure of Horse Heart Metmyoglobin
      Evans, S.V.,Brayer, G.D.
      (1990) J.Mol.Biol. 213: 885
    • Ftir Analysis of the Interaction of Azide with Horse Heart Myoglobin Variants
      Bogumil, R.,Hunter, C.L.,Maurus, R.,Tang, H.L.,Lee, H.,Lloyd, E.,Brayer, G.D.,Smith, M.,Mauk, A.G.
      (1994) Biochemistry 33: 7600
    • Horse Heart Metmyoglobin. A 2.8-A Resolution Three-Dimensional Structure Determination
      Evans, S.V.,Brayer, G.D.
      (1988) J.Biol.Chem. 263: 4263
    • Crystallization and Preliminary Diffraction Data for Horse Heart Metmyoglobin
      Sherwood, C.,Mauk, A.G.,Brayer, G.D.
      (1987) J.Mol.Biol. 193: 227
    • Three-Dimensional Structure of Cyanomet-Sulfmyoglobin C
      Evans, S.V.,Sishta, B.P.,Mauk, A.G.,Brayer, G.D.
      (1994) Proc.Natl.Acad.Sci.USA 91: 4723
    • Structural Characterization of Heme Ligation in the His64-->Tyr Variant of Myoglobin
      Maurus, R.,Bogumil, R.,Luo, Y.,Tang, H.L.,Smith, M.,Mauk, A.G.,Brayer, G.D.
      (1994) J.Biol.Chem. 269: 12606

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, and the Protein Engineering Network of Centres of Excellence, University of British Columbia, Vancouver, Canada.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
153Equus caballusMutation(s): 1 
Gene Names: MB
Find proteins for P68082 (Equus caballus)
Go to Gene View: MB
Go to UniProtKB:  P68082
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

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Download CCD File 
O4 S
 Ligand Interaction
Query on HEM

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Download CCD File 
C34 H32 Fe N4 O4
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 1.7 Å
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.566α = 90.00
b = 28.872β = 107.17
c = 35.882γ = 90.00
Software Package:
Software NamePurpose
RIGAKUdata reduction
RIGAKUdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-09-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance