2F4G

Triclinic cross-linked lysozyme soaked in bromoethanol 1M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.654 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

On the edge of the denaturation process: Application of X-ray diffraction to barnase and lysozyme cross-linked crystals with denaturants in molar concentrations.

Salem, M.Mauguen, Y.Prange, T.

(2006) Biochim.Biophys.Acta 1764: 903-912

  • DOI: 10.1016/j.bbapap.2006.02.009
  • Primary Citation of Related Structures:  
  • Also Cited By: 3KCH

  • PubMed Abstract: 
  • Structural data about the early step of protein denaturation were obtained from cross-linked crystals for two small proteins: barnase and lysozyme. Several denaturant agents like urea, bromoethanol or thiourea were used at increasing concentrations u ...

    Structural data about the early step of protein denaturation were obtained from cross-linked crystals for two small proteins: barnase and lysozyme. Several denaturant agents like urea, bromoethanol or thiourea were used at increasing concentrations up to a limit leading to crystal disruption (>or=2 to 6 M). Before the complete destruction of the crystal order started, specific binding sites were observed at the protein surfaces, an indication that the preliminary step of denaturation is the disproportion of intermolecular polar bonds to the benefit of the agent "parasiting" the surface. The analysis of the thermal factors first agree with a stabilization effect at low or moderate concentration of denaturants rapidly followed by a destabilization at specific weak points when the number of sites increase (overflooding effect).


    Organizational Affiliation

    Université René Descartes, Faculté de pharmacie, Laboratoire de cristallographie et RMN biologiques (UMR-8015, CNRS), 4 av. de l'Observatoire 75270 Paris Cedex 06, France.




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
BRJ
Query on BRJ

Download SDF File 
Download CCD File 
A
2-BROMOETHANOL
C2 H5 Br O
LDLCZOVUSADOIV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.654 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.178 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 27.130α = 88.96
b = 31.750β = 108.42
c = 34.190γ = 111.47
Software Package:
Software NamePurpose
SHELXphasing
SHELXL-97refinement
SCALEPACKdata scaling
SHELXmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-11-23 
  • Released Date: 2006-04-25 
  • Deposition Author(s): Prange, T., Salem, M.

Revision History 

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance