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2dek

From Proteopedia

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[[Image:2dek.gif|left|200px]]
 
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{{Structure
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==Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 at 1.65 A resolution==
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|PDB= 2dek |SIZE=350|CAPTION= <scene name='initialview01'>2dek</scene>, resolution 1.65&Aring;
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<StructureSection load='2dek' size='340' side='right'caption='[[2dek]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>
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<table><tr><td colspan='2'>[[2dek]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DEK FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphthine_synthase Diphthine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.98 2.1.1.98] </span>
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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]] 1.65&#8491;</td></tr>
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|GENE= dphB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
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|DOMAIN=
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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=2dek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dek OCA], [https://pdbe.org/2dek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dek RCSB], [https://www.ebi.ac.uk/pdbsum/2dek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dek ProSAT], [https://www.topsan.org/Proteins/RSGI/2dek TOPSAN]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dek OCA], [http://www.ebi.ac.uk/pdbsum/2dek PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dek RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/DPHB_PYRHO DPHB_PYRHO] S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the trimethylation of the amino group of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine. The three successive methylation reactions represent the second step of diphthamide biosynthesis.<ref>PMID:20873788</ref>
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== Evolutionary Conservation ==
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'''Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 at 1.65 A resolution'''
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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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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/2dek_consurf.spt"</scriptWhenChecked>
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2DEK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEK OCA].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: Diphthine synthase]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: Pyrococcus horikoshii]]
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</jmolCheckbox>
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[[Category: Single protein]]
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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=2dek ConSurf].
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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<div style="clear:both"></div>
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[[Category: Shimizu, K.]]
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== References ==
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[[Category: alpha/beta fold]]
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<references/>
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[[Category: antiparallel beta-sheet]]
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__TOC__
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[[Category: national project on protein structural and functional analyse]]
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</StructureSection>
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[[Category: nppsfa]]
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[[Category: Large Structures]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: Pyrococcus horikoshii OT3]]
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[[Category: rsgi]]
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[[Category: Shimizu K]]
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[[Category: structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:33:41 2008''
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Current revision

Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 at 1.65 A resolution

PDB ID 2dek

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