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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.str.2010.09.010
  • Primary Citation of Related Structures:  2XBR

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME C
A
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.147 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.770α = 90.00
b = 78.770β = 90.00
c = 37.110γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-08-10
    Type: Database references, Version format compliance