2D4J: Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution

Citation:
Acta Crystallogr. D Biol. Crystallogr. (2006) 62 p.375-382
Abstract
Two monoclinic crystals (space group P2(1)) of hen egg-white lysozyme, a type I crystal grown at room temperature in a D2O solution with pD 4.5 containing 2%(w/v) sodium nitrate and a type II crystal grown at 313 K in a 10%(w/v) sodium chloride solution with pH 7.6, were each transformed into another monoclinic crystal with the same space group by dehydration-induced phase transition. Changes in X-ray diffraction were recorded to monitor the progress of the crystal transformation, which started with the appearance of diffuse streaks. In both crystals, the intensity of h + l odd reflections gradually weakened and finally disappeared on completion of the transformation. X-ray diffraction in the intermediate state indicated the presence of lattices of both the native and transformed crystals. In the native type I crystal, two alternate conformations were observed in the main chain of the region Gly71-Asn74. One conformer bound a sodium ion which was replaced with a water molecule in the other conformer. In the transformed crystal, the sodium ion was removed and the main-chain conformation of this region was converted to that of the water-bound form. The transformed crystal diffracted to a higher resolution than the native crystal, while the peak width of the diffraction spots increased. Analysis of the thermal motion of protein molecules using the TLS model has shown that the enhancement of the diffraction power in the transformed crystal is mainly ascribable to the suppression of rigid-body motion owing to an increase in intermolecular contacts as a result of the loss of bulk solvent.
PDB ID: 2D4JDownload
MMDB ID: 40337
PDB Deposition Date: 2005/10/20
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 1.16  Å
Source Organism:
Similar Structures:
Biological Unit for 2D4J: monomeric; determined by author
Molecular Components in 2D4J
Label Count Molecule
Protein (1 molecule)
1
Lysozyme C(Gene symbol: LYZ)
Molecule annotation
Chemicals (4 molecules)
1
4
* Click molecule labels to explore molecular sequence information.

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