1JIY

CRYSTAL STRUCTURE OF TETRAGONAL LYSOZYME GROWN IN PRESENCE 20% SORBITOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The effect of stabilizing additives on the structure and hydration of proteins: a study involving tetragonal lysozyme.

Datta, S.Biswal, B.K.Vijayan, M.

(2001) Acta Crystallogr.,Sect.D 57: 1614-1620

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In order to elucidate the effect of stabilizing additives on the structure of proteins and the associated ordered water molecules in the hydration shell, the crystal structures of tetragonal lysozyme grown in the presence of sucrose, sorbitol and tre ...

    In order to elucidate the effect of stabilizing additives on the structure of proteins and the associated ordered water molecules in the hydration shell, the crystal structures of tetragonal lysozyme grown in the presence of sucrose, sorbitol and trehalose have been refined. Also refined are the structures of orthorhombic and monoclinic lysozyme grown under the conditions in which tetragonal lysozyme is normally grown. A comparison of the two sets of structures with the structure of native tetragonal lysozyme shows that the effect of the additives on the structure of the protein molecule is less than that of the normal minor changes associated with differences in molecular packing. Surprisingly, the same is true of the effect on the hydration shell, represented by the ordered water molecules attached to the protein. Thus, it appears that the cause of the stabilizing effect of the additives needs to be sought outside the immediate neighbourhood of the protein molecule. Sorbitol and trehalose do not coherently interact with the protein. One sucrose molecule binds at the active-site cleft of the enzyme.


    Related Citations: 
    • Hydration, Mobility and Accessibility of Lysozyme: Strucutres of a Ph 6.5 Orthorhombic Form and its Low-Humidity Variant and a Comparative Study Involving 20 Crystallographically Independent Molecules
      Biswal, B.K.,Sukumar, N.,Vijayan, M.
      (2000) Acta Crystallogr.,Sect.D 56: 1110
    • Protein Hydration and Water Structure: X-Ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content
      Madhusudan, K.,Kodandapani, R.,Vijayan, M.
      (1993) Acta Crystallogr.,Sect.D 49: 234


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
A
129Gallus gallusMutation(s): 0 
Gene 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: 1.9 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.189 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.340α = 90.00
b = 79.340β = 90.00
c = 37.900γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
AMoREphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-10-04
    Type: Refinement description