5I54

Exploring onset of lysozyme denaturation by urea - soak period 4 hours


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.608 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


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Literature

Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation

Raskar, T.Khavnekar, S.Hosur, M.

(2016) Sci Rep 6: 32277-32277

  • DOI: 10.1038/srep32277
  • Primary Citation of Related Structures:  5I4W, 5I4X, 5I4Y, 5I53

  • PubMed Abstract: 
  • Temporal binding of urea to lysozyme was examined using X-ray diffraction of single crystals of urea/lysozyme complexes prepared by soaking native lysozyme crystals in solutions containing 9 M urea. Four different soak times of 2, 4, 7 and 10 hours w ...

    Temporal binding of urea to lysozyme was examined using X-ray diffraction of single crystals of urea/lysozyme complexes prepared by soaking native lysozyme crystals in solutions containing 9 M urea. Four different soak times of 2, 4, 7 and 10 hours were used. The five crystal structures (including the native lysozyme), refined to 1.6 Å resolution, reveal that as the soaking time increased, more and more first-shell water molecules are replaced by urea. The number of hydrogen bonds between urea and the protein is similar to that between protein and water molecules replaced by urea. However, the number of van der Waals contacts to protein from urea is almost double that between the protein and the replaced water. The hydrogen bonding and van der Waals interactions are initially greater with the backbone and later with side chains of charged residues. Urea altered the water-water hydrogen bond network both by replacing water solvating hydrophobic residues and by shortening the first-shell intra-water hydrogen bonds by 0.2 Å. These interaction data suggest that urea uses both 'direct' and 'indirect' mechanisms to unfold lysozyme. Specific structural changes constitute the first steps in lysozyme unfolding by urea.


    Organizational Affiliation

    Tata Memorial Centre/Advanced Centre for Treatment Research and Education in Cancer, Kharghar, Navi Mumbai, 410210, India.




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
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
URE
Query on URE

Download SDF File 
Download CCD File 
A
UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.608 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.040α = 90.00
b = 79.040β = 90.00
c = 36.600γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release