2W6W

Crystal structure of recombinant Sperm Whale Myoglobin under 1atm of Xenon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

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This is version 1.2 of the entry. See complete history


Literature

Pattern of Cavities in Globins: The Case of Human Hemoglobin.

Savino, C.Miele, A.E.Draghi, F.Johnson, K.A.Sciara, G.Brunori, M.Vallone, B.

(2009) Biopolymers 91: 1097

  • DOI: 10.1002/bip.21201
  • Primary Citation of Related Structures:  
    2W72, 2W6V, 2W6W

  • PubMed Abstract: 
  • Our aim is to shed light on the conservation of potential ligand docking sites that play an important role in ligand dynamics of globins by using the technique of filling internal cavities naturally present in hemoglobin and myoglobin with xenon atoms. In particular, we present the high resolution structures of the Xe-adduct of deoxygenated wild type human hemoglobin and a quadruple mutant (L(B10)Y and H(E7)Q in alpha and beta chains) ...

    Our aim is to shed light on the conservation of potential ligand docking sites that play an important role in ligand dynamics of globins by using the technique of filling internal cavities naturally present in hemoglobin and myoglobin with xenon atoms. In particular, we present the high resolution structures of the Xe-adduct of deoxygenated wild type human hemoglobin and a quadruple mutant (L(B10)Y and H(E7)Q in alpha and beta chains). For the sake of comparison we also determined under the same experimental conditions the xenon complex of wild type sperm whale myoglobin. The analysis revealed that the number and position of Xe binding cavities are different in the alpha and beta subunits, the latter being more similar to myoglobin. Notably, no proximal Xe docking site was detected in hemoglobin, at variance with myoglobin. The pattern of internal cavities accessibility and affinity for xenon suggests a different role for the dynamics of ligand migration in the two types of hemoglobin chains as compared to myoglobin. The number and position of hydrophobic cavities in hemoglobin are briefly discussed also in comparison with the data available for other members of the globin superfamily.


    Organizational Affiliation

    University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy. linda.savino@uniroma1.it



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MYOGLOBINA154Physeter catodonMutation(s): 0 
Gene Names: MB
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.626α = 90
b = 90.626β = 90
c = 45.505γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-10-26
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description