2d8p: Difference between revisions

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-{{Seed}}
-[[Image:2d8p.png|left|200px]]
-<!--
+==Structure of HYPER-VIL-thaumatin==
-The line below this paragraph, containing "STRUCTURE_2d8p", creates the "Structure Box" on the page.
+<StructureSection load='2d8p' size='340' side='right'caption='[[2d8p]], [[Resolution|resolution]] 2.30&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'>[[2d8p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thaumatococcus_daniellii Thaumatococcus daniellii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D8P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D8P 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]] 2.3&#8491;</td></tr>
--->
+<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>
-{{STRUCTURE_2d8p|  PDB=2d8p  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d8p OCA], [https://pdbe.org/2d8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d8p RCSB], [https://www.ebi.ac.uk/pdbsum/2d8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d8p 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/d8/2d8p_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=2d8p 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 HYPER-VIL-thaumatin===
+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 2d8p" 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]]
-D8P is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thaumatococcus_daniellii Thaumatococcus daniellii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D8P OCA].
-==Reference==
-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://www.ncbi.nlm.nih.gov/pubmed/16510975 16510975]
-[[Category: Single protein]]
 [[Category: Thaumatococcus daniellii]]
-[[Category: Hasegawa, T.]]
+[[Category: Hasegawa T]]
-[[Category: Miyatake, H.]]
+[[Category: Miyatake H]]
-[[Category: Yamano, A.]]
+[[Category: Yamano A]]
-[[Category: Iodo-tyrosine]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 12:49:14 2008''