1LJI

CRYSTAL STRUCTURE OF MONOCLINIC LYSOZYME GROWN IN PRESENCE 10% SORBITOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


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.,Sect.D 58: 1162-1167

  • Primary Citation of Related Structures:  1LJ3, 1LJ4, 1LJE, 1LJF, 1LJG, 1LJH, 1LJJ, 1LJK

  • 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 di ...

    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.,Sect.D 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.,Sect.D 52: 1067


    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 C
A, B
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download SDF File 
Download CCD File 
A, B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 27.783α = 90.00
b = 62.707β = 90.73
c = 60.285γ = 90.00
Software Package:
Software NamePurpose
AUTOMARdata reduction
CNSrefinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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