2d4j
From Proteopedia
(New page: 200px<br /><applet load="2d4j" size="450" color="white" frame="true" align="right" spinBox="true" caption="2d4j, resolution 1.16Å" /> '''Transformed monoclin...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:2d4j.gif|left|200px]]<br /><applet load="2d4j" size=" | + | [[Image:2d4j.gif|left|200px]]<br /><applet load="2d4j" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2d4j, resolution 1.16Å" /> | caption="2d4j, resolution 1.16Å" /> | ||
'''Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution'''<br /> | '''Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Two monoclinic crystals (space group P2(1)) of hen egg-white lysozyme, a | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 2D4J is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with NO3 and DOD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] Full crystallographic information is available from [http:// | + | 2D4J is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with <scene name='pdbligand=NO3:'>NO3</scene> and <scene name='pdbligand=DOD:'>DOD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4J OCA]. |
==Reference== | ==Reference== | ||
| Line 22: | Line 22: | ||
[[Category: tls analysis]] | [[Category: tls analysis]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:55:18 2008'' |
Revision as of 14:55, 21 February 2008
|
Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution
Overview
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.
About this Structure
2D4J is a Single protein structure of sequence from Gallus gallus with and as ligands. Active as Lysozyme, with EC number 3.2.1.17 Full crystallographic information is available from OCA.
Reference
Structural phase transition of monoclinic crystals of hen egg-white lysozyme., Harata K, Akiba T, Acta Crystallogr D Biol Crystallogr. 2006 Apr;62(Pt 4):375-82. Epub 2006, Mar 18. PMID:16552138
Page seeded by OCA on Thu Feb 21 16:55:18 2008
Categories: Gallus gallus | Lysozyme | Single protein | Akiba, T. | Harata, K. | DOD | NO3 | Phase transition | Rigid-body motion | Tls analysis
