1XEJ

THE CRYSTAL STRUCTURES OF LYSOZYME AT VERY LOW LEVELS OF HYDRATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Role of water in plasticity, stability, and action of proteins: the crystal structures of lysozyme at very low levels of hydration.

Nagendra, H.G.Sukumar, N.Vijayan, M.

(1998) Proteins 32: 229-240

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Earlier studies involving water-mediated transformations in lysozyme and ribonuclease A have shown that the overall movements in the protein molecule consequent to the reduction in the amount of surrounding water are similar to those that occur durin ...

    Earlier studies involving water-mediated transformations in lysozyme and ribonuclease A have shown that the overall movements in the protein molecule consequent to the reduction in the amount of surrounding water are similar to those that occur during enzyme action, thus highlighting the relationship among hydration, plasticity, and action of these enzymes. Monoclinic lysozyme retains its crystallinity even when the level of hydration is reduced further below that necessary for activity (about 0.2 gram of water per gram of protein). In order to gain insights into the role of water in the stability and the plasticity of the protein molecule and the geometrical basis for the loss of activity that accompanies dehydration, the crystal structures of monoclinic lysozyme with solvent contents of 17.6%, 16.9%, and 9.4% were determined and refined. A detailed comparison of these forms with the normally hydrated forms show that the C-terminal segment (residues 88-129) of domain I and the main loop (residues 65-73) in domain II exhibit large deviations in atomic positions when the solvent content is reduced, although the three-dimensional structure is essentially preserved. Many crucial water bridges between different regions of the molecule are conserved in spite of differences in detail, even when the level of hydration is reduced well below that required for activity. The loss of activity that accompany dehydration appears to be caused by the removal of functionally important water molecules from the active-site region and the reduction in the size of the substrate binding cleft.


    Related Citations: 
    • Characterization of Lysozyme Crystals with Unusually Low Solvent Content
      Nagendra, H.G.,Sudarsanakumar, C.,Vijayan, M.
      (1995) Acta Crystallogr.,Sect.D 51: 390
    • Comparison of Radiation Induced Decay and Structure Refinement from X-Ray Data Collected from Lysozyme Crystals at Low and Ambient Temperatures
      Young, A.C.M.,Dewan, J.C.,Nave, C.,Tilton, R.F.
      (1993) J.Appl.Crystallogr. 26: 309
    • Protein Hydration and Water Structure: X-Ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content
      Madhusudan,Kodandapani, R.,Vijayan, M.
      (1993) Acta Crystallogr.,Sect.D 49: 234
    • Crystal Structure of Low Humidity Tetragonal Lysozyme at 2.1-A Resolution. Variability in Hydration Shell and its Structural Consequences
      Kodandapani, R.,Suresh, C.G.,Vijayan, M.
      (1990) J.Biol.Chem. 265: 16126


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 26.345α = 90.00
b = 55.885β = 109.98
c = 31.550γ = 90.00
Software Package:
Software NamePurpose
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
XENGENdata scaling
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2016-10-26
    Type: Other