1LJH

CRYSTAL STRUCTURE OF MONOCLINIC LYSOZYME GROWN IN PRESENCE OF 5% GLYCEROL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

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This is version 1.3 of the entry. See complete history


Literature

Effect of stabilizing additives on the structure and hydration of proteins: a study involving monoclinic lysozyme.

Saraswathi, N.T.Sankaranarayanan, R.Vijayan, M.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1162-1167

  • DOI: 10.1107/s0907444902007126
  • Primary Citation of Related Structures:  
    1LJF, 1LJE, 1LJK, 1LJJ, 1LJI, 1LJH, 1LJG, 1LJ4, 1LJ3

  • PubMed Abstract: 
  • In pursuance of a long-range programme on the hydration, mobility and action of proteins, the structural basis of the stabilizing effect of sugars and polyols is being investigated. With two crystallographically independent molecules with slightly different packing environments in the crystal, monoclinic lysozyme constitutes an ideal system for exploring the problem ...

    In pursuance of a long-range programme on the hydration, mobility and action of proteins, the structural basis of the stabilizing effect of sugars and polyols is being investigated. With two crystallographically independent molecules with slightly different packing environments in the crystal, monoclinic lysozyme constitutes an ideal system for exploring the problem. The differences in the structure and hydration of the two molecules provide a framework for examining the changes caused by stabilizing additives. Monoclinic crystals were grown under native conditions and also in the presence of 10% sucrose, 15% trehalose, 10% trehalose, 10% sorbitol and 5% glycerol. The crystal structures were refined at resolutions ranging from 1.8 to 2.1 A. The average B values, and hence the mobility of the structure, are lower in the presence of additives than in the native crystals. However, a comparison of the structures indicates that the effect of the additives on the structure and the hydration shell around the protein molecule is considerably less than that caused by differences in packing. It is also less than that caused by the replacement of NaNO(3) by NaCl as the precipitant in the crystallization experiments. This result is not in conformity with the commonly held belief that additives exert their stabilizing effect through the reorganization of the hydration shell, at least as far as the ordered water molecules are concerned.


    Related Citations: 
    • 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 D Biol Crystallogr 57: 1614
    • An X-Ray Analysis of Native Monoclinic Lysozyme. A Case Study on the Reliability of Refined Protein Structures and a Comparison with the Low-Humidity Form in Relation to Mobility and Enzyme Action
      Nagendra, H.G., Sudarsanakumar, C., Vijayan, M.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 1067

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme CA, B129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.909α = 90
b = 62.808β = 90.56
c = 60.331γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-19
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description