2d98

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(New page: 200px<br /><applet load="2d98" size="450" color="white" frame="true" align="right" spinBox="true" caption="2d98, resolution 2.00&Aring;" /> '''Structure of VIL (ex...)
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[[Image:2d98.gif|left|200px]]<br /><applet load="2d98" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2d98, resolution 2.00&Aring;" />
 
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'''Structure of VIL (extra KI/I2 added)-xylanase'''<br />
 
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==Overview==
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==Structure of VIL (extra KI/I2 added)-xylanase==
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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.
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<StructureSection load='2d98' size='340' side='right'caption='[[2d98]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2d98]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_reesei Trichoderma reesei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D98 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D98 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d98 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d98 OCA], [https://pdbe.org/2d98 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d98 RCSB], [https://www.ebi.ac.uk/pdbsum/2d98 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d98 ProSAT]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d9/2d98_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d98 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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<ref>PMID:16510975</ref>
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2D98 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina] with IOD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2D98 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16510975 16510975]
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</div>
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[[Category: Endo-1,4-beta-xylanase]]
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<div class="pdbe-citations 2d98" style="background-color:#fffaf0;"></div>
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[[Category: Hypocrea jecorina]]
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== References ==
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[[Category: Single protein]]
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<references/>
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[[Category: Hasegawa, T.]]
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__TOC__
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[[Category: Miyatake, H.]]
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</StructureSection>
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[[Category: Yamano, A.]]
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[[Category: Large Structures]]
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[[Category: IOD]]
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[[Category: Trichoderma reesei]]
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[[Category: iodo-tyrosine]]
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[[Category: Hasegawa T]]
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[[Category: vaporizing iodine labeling(vil)]]
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[[Category: Miyatake H]]
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[[Category: Yamano A]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:29:49 2007''
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Current revision

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

PDB ID 2d98

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