2d98: Difference between revisions

Revision as of 23:55, 3 May 2008

Structure of VIL (extra KI/I2 added)-xylanase

OverviewOverview

New techniques are presented for the preparation of iodine derivatives, involving vapour diffusion of iodine. Firstly, in the vaporizing iodine labelling (VIL) technique, a small amount of KI/I(2) solution is enclosed in a crystallization well, with the result that gaseous I(2) molecules diffuse into the crystallization droplets without exerting substantial changes in ionic strength in the target crystals. Once they have diffused into the droplet, the I(2) molecules sometimes iodinate accessible tyrosines at ortho positions. Secondly, when iodination is insufficient, the hydrogen peroxide VIL (HYPER-VIL) technique can be further applied to increase the iodination ratio by the addition of a small droplet of hydrogen peroxide (H(2)O(2)) to the crystallization well; the gaseous H(2)O(2) also diffuses into the crystallization droplet to emphasize the iodination. These techniques are most effective for phase determination when coupled with softer X-rays, such as those from Cu Kalpha or Cr Kalpha radiation. The effectiveness of these techniques was assessed using five different crystals. Four of the crystals were successfully iodinated, providing sufficient phasing power for structure determination.

About this StructureAbout this Structure

2D98 is a Single protein structure of sequence from Hypocrea jecorina. Full crystallographic information is available from OCA.

ReferenceReference

New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL)., Miyatake H, Hasegawa T, Yamano A, Acta Crystallogr D Biol Crystallogr. 2006 Mar;62(Pt 3):280-9. Epub 2006, Feb 22. PMID:16510975 Page seeded by OCA on Sat May 3 23:55:34 2008

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OCA

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 [[Image:2d98.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 2d98 |SIZE=350|CAPTION= <scene name='initialview01'>2d98</scene>, resolution 2.00&Aring;
+The line below this paragraph, containing "STRUCTURE_2d98", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=IYR:3-IODO-TYROSINE'>IYR</scene>, <scene name='pdbligand=TYI:3,5-DIIODOTYROSINE'>TYI</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_2d98|  PDB=2d98  |  SCENE=  }}
-|RELATEDENTRY=[[2d8o|2D8O]], [[2d8p|2D8P]], [[2d8w|2D8W]], [[2d91|2D91]], [[2d97|2D97]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d98 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d98 OCA], [http://www.ebi.ac.uk/pdbsum/2d98 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2d98 RCSB]</span>
-}}
 '''Structure of VIL (extra KI/I2 added)-xylanase'''
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 [[Category: Miyatake, H.]]
 [[Category: Yamano, A.]]
-[[Category: iodo-tyrosine]]
+[[Category: Iodo-tyrosine]]
-[[Category: vaporizing iodine labeling(vil)]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 23:55:34 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:31:36 2008''