2e6u: Difference between revisions

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-[[Image:2e6u.gif|left|200px]]<br /><applet load="2e6u" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2e6u, resolution 1.80&Aring;" />
-'''Crystal structure of hypothetical protein PH1109 from Pyrococcus horikoshii'''<br />
-==Overview==
+==Crystal structure of hypothetical protein PH1109 from Pyrococcus horikoshii==
-A novel and easy crystal-mounting technique was developed for the sulfur SAD method using Cr Kalpha radiation (2.29 A). Using this technique, the cryo-buffer and cryoloop around the protein crystal can be removed before data collection in order to eliminate their X-ray absorption. The superiority and reproducibility of the data sets with this mounting technique were demonstrated using tetragonal hen egg-white lysozyme crystals. The structure of a novel protein, PH1109, from Pyrococcus horikoshii OT3 was solved using this technique. At the wavelength of Cr Kalpha radiation, the anomalous signal |DeltaF|/|F| of PH1109 is expected to be 1.72% as this protein of 144 residues includes four methionines and two cysteines. Sulfur SAD phasing was performed using SHELXD and SHELXE. In the case of the data set obtained using this novel crystal-mounting technique, 54.9% of all residues were built with side chains automatically by RESOLVE. On the other hand, only 16.0% were built with side chains for the data set collected using the standard cryoloop. These results indicated that this crystal-mounting technique was superior to the standard loop-mounting method for the measurement of small anomalous differences at longer wavelength and yielded better results in sulfur-substructure solution and initial phasing. The present study demonstrates that the sulfur SAD method with a chromium source becomes enhanced and more practical for macromolecular structure determination using the new crystal-mounting technique.
+<StructureSection load='2e6u' size='340' side='right'caption='[[2e6u]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[2e6u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2czz 2czz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E6U FirstGlance]. <br>
-E6U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] with <scene name='pdbligand=CA:'>CA</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=COA:'>COA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 2CZZ. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E6U OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2e6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6u OCA], [https://pdbe.org/2e6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e6u RCSB], [https://www.ebi.ac.uk/pdbsum/2e6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e6u ProSAT]</span></td></tr>
-Structure determination of a novel protein by sulfur SAD using chromium radiation in combination with a new crystal-mounting method., Kitago Y, Watanabe N, Tanaka I, Acta Crystallogr D Biol Crystallogr. 2005 Aug;61(Pt 8):1013-21. Epub 2005, Jul 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16041065 16041065]
+</table>
-[[Category: Pyrococcus horikoshii]]
+== Function ==
-[[Category: Single protein]]
+[https://www.uniprot.org/uniprot/O58836_PYRHO O58836_PYRHO]
-[[Category: Kitago, Y.]]
+== Evolutionary Conservation ==
-[[Category: Min, Y.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Tanaka, I.]]
+Check<jmol>
-[[Category: Watanabe, N.]]
+  <jmolCheckbox>
-[[Category: CA]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e6/2e6u_consurf.spt"</scriptWhenChecked>
-[[Category: CL]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: COA]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: coa binding]]
+  </jmolCheckbox>
-[[Category: rossmann-like]]
+</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=2e6u ConSurf].
-[[Category: structural genomics consortium for research on gene expression system]]
+<div style="clear:both"></div>
+__TOC__
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:06:40 2008''
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Pyrococcus horikoshii OT3]]
+[[Category: Kitago Y]]
+[[Category: Min Y]]
+[[Category: Tanaka I]]
+[[Category: Watanabe N]]