2XBS

Raman crystallography of Hen White Egg Lysozyme - High X-ray dose (16 MGy)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

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This is version 1.2 of the entry. See complete history


Literature

Raman Assisted Crystallography Reveals a Mechanism of X-Ray Induced Reversible Disulfide Radical Formation

Carpentier, P.Royant, A.Weik, M.Bourgeois, D.

(2010) Structure 18: 1410

  • DOI: https://doi.org/10.1016/j.str.2010.09.010
  • Primary Citation of Related Structures:  
    2XBR, 2XBS

  • PubMed Abstract: 

    X-ray-induced chemistry modifies biological macromolecules structurally and functionally, even at cryotemperatures. The mechanisms of x-radiation damage in colored or redox proteins have often been investigated by combining X-ray crystallography with in crystallo-ultraviolet-visible spectroscopy. Here, we used Raman microspectrophotometry to follow the onset of damage in crystalline lysozyme, notably that of disulfide bond breakage. The dose-dependent Raman spectra are consistent with a kinetic model for the rupture of disulfide bonds suggesting the rapid build up of an anionic radical intermediate. This intermediate may either revert back to the oxidized state or evolve toward protonated radical species or cleaved products. The data strongly suggest that back conversion of the anionic radical is significantly accelerated by X-rays, revealing an X-ray-induced "repair" mechanism. The possibility of X-ray-induced chemical repair is an important feature to take into account when assessing radiation damage in macromolecules.


  • Organizational Affiliation

    Laboratoire de Cristallogenèse et Cristallographie des Protéines, IBS, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, Université Joseph Fourier, 41 Rue Jules Horowitz, F-38027 Grenoble, France. philippe.carpentier@ibs.fr


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LYSOZYME C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.77α = 90
b = 78.77β = 90
c = 37.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-08-10
    Changes: Database references, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description