2d97: Difference between revisions

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-{{Seed}}
-[[Image:2d97.png|left|200px]]
-<!--
+==Structure of VIL-xylanase==
-The line below this paragraph, containing "STRUCTURE_2d97", creates the "Structure Box" on the page.
+<StructureSection load='2d97' size='340' side='right'caption='[[2d97]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2d97]] 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=2D97 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D97 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.01&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IYR:3-IODO-TYROSINE'>IYR</scene>, <scene name='pdbligand=TYI:3,5-DIIODOTYROSINE'>TYI</scene></td></tr>
-{{STRUCTURE_2d97|  PDB=2d97  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d97 OCA], [https://pdbe.org/2d97 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d97 RCSB], [https://www.ebi.ac.uk/pdbsum/2d97 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d97 ProSAT]</span></td></tr>
+</table>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d9/2d97_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2d97 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===Structure of VIL-xylanase===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16510975}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2d97" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16510975 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16510975}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-D97 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D97 OCA].
+[[Category: Trichoderma reesei]]
+[[Category: Hasegawa T]]
-==Reference==
+[[Category: Miyatake H]]
-<ref group="xtra">PMID:16510975</ref><references group="xtra"/>
+[[Category: Yamano A]]
-[[Category: Endo-1,4-beta-xylanase]]
-[[Category: Hypocrea jecorina]]
-[[Category: Hasegawa, T.]]
-[[Category: Miyatake, H.]]
-[[Category: Yamano, A.]]
-[[Category: Iodo-tyrosine]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 02:07:20 2009''