1DXD

Photolyzed CO complex of Myoglobin Mb-YQR at 20K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.169 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.133 (Depositor), 0.140 (DCC) 

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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

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

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

(2000) Proc Natl Acad Sci U S A 97: 2058

  • DOI: https://doi.org/10.1073/pnas.040459697
  • Primary Citation of Related Structures:  
    1DXC, 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MYOGLOBIN154Physeter macrocephalusMutation(s): 4 
EC: 1.11.1 (UniProt), 1.7 (UniProt)
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: 1.40 Å
  • R-Value Free:  0.169 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.133 (Depositor), 0.140 (DCC) 
Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.493α = 90
b = 90.493β = 90
c = 45.283γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-27
    Type: Initial release
  • Version 1.1: 2012-11-28
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other