1LJ4

CRYSTAL STRUCTURE OF MONOCLINIC LYSOZYME GROWN AT PH 4.6

DOI: 10.2210/pdb1LJ4/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2002-04-19 Released: 2002-10-19
Deposition Author(s): Saraswathi, N.T., Sankaranarayanan, R., Vijayan, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.230
R-Value Work: 0.185
R-Value Observed: 0.185

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 D Biol Crystallogr 58: 1162-1167

PubMed: 12077436 Search on PubMed
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. 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
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A, B	129	Gallus gallus	Mutation(s): 0 Gene Names: LYZ EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [A] SDF format, chain E [A] SDF format, chain F [B] SDF format, chain G [B] MOL2 format, chain C [A] MOL2 format, chain D [A] MOL2 format, chain E [A] MOL2 format, chain F [B] MOL2 format, chain G [B]	A, B	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Ligand Interaction