1DXC

CO complex of Myoglobin Mb-YQR at 100K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Role of Cavities in Protein Dynamics: Crystal Structure of a Novel Photolytic Intermediate of Myoglobin

Brunori, M.Vallone, B.Cutruzzola, F.Travaglini-Allocatelli, C.Berendzen, J.Chu, K.Sweet, R.M.Schlichting, I.

(2000) Proc.Natl.Acad.Sci.USA 97: 2058

  • DOI: 10.1073/pnas.040459697
  • Primary Citation of Related Structures:  1DXD

  • PubMed Abstract: 
  • We determined the structure of the photolytic intermediate of a sperm whale myoglobin (Mb) mutant called Mb-YQR [Leu-(B10)-->Tyr; His(E7)-->Gln; Thr(E10)-->Arg] to 1.4-A resolution by ultra-low temperature (20 K) x-ray diffraction. Starting with the ...

    We determined the structure of the photolytic intermediate of a sperm whale myoglobin (Mb) mutant called Mb-YQR [Leu-(B10)-->Tyr; His(E7)-->Gln; Thr(E10)-->Arg] to 1.4-A resolution by ultra-low temperature (20 K) x-ray diffraction. Starting with the CO complex, illumination leads to photolysis of the Fe-CO bond, and migration of the photolyzed carbon monoxide (CO*) to a niche in the protein 8.1 A from the heme iron; this cavity corresponds to that hosting an atom of Xe when the crystal is equilibrated with xenon gas at 7 atmospheres [Tilton, R. F., Jr., Kuntz, I. D. & Petsko, G. A. (1984) Biochemistry 23, 2849-2857]. The site occupied by CO* corresponds to that predicted by molecular dynamics simulations previously carried out to account for the NO geminate rebinding of Mb-YQR observed in laser photolysis experiments at room temperature. This secondary docking site differs from the primary docking site identified by previous crystallographic studies on the photolyzed intermediate of wild-type sperm whale Mb performed at cryogenic temperatures [Teng et al. (1994) Nat. Struct. Biol. 1, 701-705] and room temperature [Srajer et al. (1996) Science 274, 1726-1729]. Our experiment shows that the pathway of a small molecule in its trajectory through a protein may be modified by site-directed mutagenesis, and that migration within the protein matrix to the active site involves a limited number of pre-existing cavities identified in the interior space of the protein.


    Related Citations: 
    • High-Level Expression of Sperm Whale Myoglobin in Escherichia Coli
      Springer, B.A.,Sligar, S.G.
      (1987) Proc.Natl.Acad.Sci.USA 84: 8961
    • Crystal Structure of Photolysed Carbonmonoxy-Myoglobin
      Schlichting, I.,Berendzen, J.,Juniorsweet, R.M.G.N.P.
      (1994) Nature 371: 808
    • Crystal Structure of Myoglobin from a Synthetic Gene
      Juniorarduini, R.M.G.N.P.,Springer, B.A.,Sligar, S.G.
      (1990) Proteins: Struct.,Funct., Genet. 7: 358
    • Structural Dynamics of Liganddiffusion in the Protein Matrix: A Study on a New Myoglobin Mutant Y (B10) Q(E7) R(E10)
      Brunori, M.,Cutruzzola, F.,Savino, C.,Travaglini-Allocatelli, C.,Vallone, B.,Gibson, Q.H.
      (1999) Biophys.J. 76: 1259


    Organizational Affiliation

    Department of Biochemical Sciences, Consiglio Nazionale delle Ricerche Centre of Molecular Biology, University "La Sapienza," 00185 Rome, Italy. brunori@axrma.uniroma1.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
154Physeter catodonGene Names: MB
Find proteins for P02185 (Physeter catodon)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
A
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.128 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 90.610α = 90.00
b = 90.610β = 90.00
c = 45.330γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-02
    Type: Initial release
  • Version 1.1: 2012-11-28
    Type: Database references, Derived calculations, Non-polymer description, Other, Version format compliance