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New page: left|200px<br /><applet load="1vbk" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vbk, resolution 1.90Å" /> '''Crystal structure of...
 
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[[Image:1vbk.gif|left|200px]]<br /><applet load="1vbk" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1vbk, resolution 1.90&Aring;" />
'''Crystal structure of PH1313 from Pyrococcus horikoshii Ot3'''<br />


==Overview==
==Crystal structure of PH1313 from Pyrococcus horikoshii Ot3==
The putative thiamine-biosynthesis protein PH1313 from Pyrococcus, horikoshii OT3 has been overexpressed and purified. Crystallization was, performed by the oil-microbatch method using 28%(v/v), 2-methyl-2,4-pentanediol as a precipitant at 291 K. A native X-ray, diffraction data set at 1.9 A resolution and a single anomalous dispersion, data set from a selenomethionine-derivative crystal at 2.1 A resolution, were collected using synchrotron radiation at 100 K. The native crystal, belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell, parameters a = 71.7, b = 71.2, c = 141.8 A.
<StructureSection load='1vbk' size='340' side='right'caption='[[1vbk]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1vbk]] 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=1VBK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VBK FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbk OCA], [https://pdbe.org/1vbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vbk RCSB], [https://www.ebi.ac.uk/pdbsum/1vbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vbk ProSAT], [https://www.topsan.org/Proteins/RSGI/1vbk TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O59053_PYRHO O59053_PYRHO]
== 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/vb/1vbk_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1vbk ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3 has been overexpressed and purified. Crystallization was performed by the oil-microbatch method using 28%(v/v) 2-methyl-2,4-pentanediol as a precipitant at 291 K. A native X-ray diffraction data set at 1.9 A resolution and a single anomalous dispersion data set from a selenomethionine-derivative crystal at 2.1 A resolution were collected using synchrotron radiation at 100 K. The native crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 71.7, b = 71.2, c = 141.8 A.


==About this Structure==
Purification, crystallization and preliminary crystallographic analysis of the putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3.,Sugahara M, Murai S, Sugahara M, Kunishima N Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Jan 1;63(Pt, 1):56-8. Epub 2006 Dec 22. PMID:17183176<ref>PMID:17183176</ref>
1VBK 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 MRD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VBK OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Purification, crystallization and preliminary crystallographic analysis of the putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3., Sugahara M, Murai S, Sugahara M, Kunishima N, Acta Crystallograph Sect F Struct Biol Cryst Commun. 2007 Jan 1;63(Pt, 1):56-8. Epub 2006 Dec 22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17183176 17183176]
</div>
[[Category: Pyrococcus horikoshii]]
<div class="pdbe-citations 1vbk" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
== References ==
[[Category: Kunishima, N.]]
<references/>
[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
__TOC__
[[Category: Sugahara, M.]]
</StructureSection>
[[Category: MRD]]
[[Category: Large Structures]]
[[Category: national project on protein structural and functional analyses]]
[[Category: Pyrococcus horikoshii OT3]]
[[Category: nppsfa]]
[[Category: Kunishima N]]
[[Category: pyrococcus horikoshii]]
[[Category: Sugahara M]]
[[Category: riken structural genomics/proteomics initiative]]
[[Category: rsgi]]
[[Category: structural genomics]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:02:21 2007''

Latest revision as of 00:01, 28 December 2023

Crystal structure of PH1313 from Pyrococcus horikoshii Ot3

1vbk, resolution 1.90Å

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