1YL1

Effect of alcohols on protein hydration


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Effect of alcohols on protein hydration: crystallographic analysis of hen egg-white lysozyme in the presence of alcohols.

Deshpande, A.Nimsadkar, S.Mande, S.C.

(2005) Acta Crystallogr.,Sect.D 61: 1005-1008

  • DOI: 10.1107/S0907444905009364
  • Primary Citation of Related Structures:  1YKX, 1YKY, 1YKZ, 1YL0, 1Z55
  • Also Cited By: 3RNX

  • PubMed Abstract: 
  • Organic solvents are known to bring about dehydration of proteins, the molecular basis of which has remained uncharacterized. The dehydration effect in many cases leads to eventual unfolding of proteins through the macroscopic solvent effect. In some ...

    Organic solvents are known to bring about dehydration of proteins, the molecular basis of which has remained uncharacterized. The dehydration effect in many cases leads to eventual unfolding of proteins through the macroscopic solvent effect. In some cases, the organic solvent molecules also bind to protein surfaces, thereby forcing local unfolding. The X-ray structure of hen egg-white lysozyme co-crystallized in the presence of alcohols with varying hydrophobicities has been studied. It was noticed that although the alcohols have very little effect on the conformation of the overall protein structure, they profoundly affect protein hydration and disorder of the bound waters. Systematic analysis of the water structure around the lysozyme molecule suggests that an increasing order of hydrophobicity of alcohols is directly proportional to the higher number of weakly bound waters in the protein. As anticipated, the water molecules in the native structure with high temperature factors (>/=40 A(2)) attain higher disorder in the presence of alcohols. It is believed that the disorder induced in the water molecules is a direct consequence of alcohol binding.


    Organizational Affiliation

    Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
X
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
ETF
Query on ETF

Download SDF File 
Download CCD File 
X
TRIFLUOROETHANOL
C2 H3 F3 O
RHQDFWAXVIIEBN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
X
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.288α = 90.00
b = 79.288β = 90.00
c = 37.957γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance