1v96: Difference between revisions

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New page: left|200px<br /><applet load="1v96" size="450" color="white" frame="true" align="right" spinBox="true" caption="1v96, resolution 1.75Å" /> '''Crystal structure of...
 
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[[Image:1v96.gif|left|200px]]<br /><applet load="1v96" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1v96, resolution 1.75&Aring;" />
'''Crystal structure of hypothetical protein of unknown function from pyrococcus horikoshii OT3'''<br />


==Overview==
==Crystal structure of hypothetical protein of unknown function from pyrococcus horikoshii OT3==
The Pyrococcus horikoshii OT3 protein PH0500 is highly conserved within, the Pyrococcus genus of hyperthermophilic archaea and shows low amino-acid, sequence similarity with a family of PIN-domain proteins. The protein has, been expressed, purified and crystallized in two crystal forms: PH0500-I, and PH0500-II. The structure was determined at 2.0 A by the multiple, anomalous dispersion method using a selenomethionyl derivative of crystal, form PH0500-I (PH0500-I-Se). The structure of PH0500-I has been refined at, 1.75 A resolution to an R factor of 20.9% and the structure of PH0500-II, has been refined at 2.0 A resolution to an R factor of 23.4%. In both, crystal forms as well as in solution the molecule appears to be a dimer., Searches of the databases for protein-fold similarities confirmed that the, PH0500 protein is a PIN-domain protein with possible exonuclease activity, and involvement in DNA or RNA editing.
<StructureSection load='1v96' size='340' side='right'caption='[[1v96]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1v96]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V96 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V96 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]] 1.75&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=1v96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v96 OCA], [https://pdbe.org/1v96 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v96 RCSB], [https://www.ebi.ac.uk/pdbsum/1v96 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v96 ProSAT], [https://www.topsan.org/Proteins/RSGI/1v96 TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/VAPC4_PYRHO VAPC4_PYRHO] Toxic component of a toxin-antitoxin (TA) module. An RNase.[HAMAP-Rule:MF_00265]
== 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/v9/1v96_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=1v96 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Pyrococcus horikoshii OT3 protein PH0500 is highly conserved within the Pyrococcus genus of hyperthermophilic archaea and shows low amino-acid sequence similarity with a family of PIN-domain proteins. The protein has been expressed, purified and crystallized in two crystal forms: PH0500-I and PH0500-II. The structure was determined at 2.0 A by the multiple anomalous dispersion method using a selenomethionyl derivative of crystal form PH0500-I (PH0500-I-Se). The structure of PH0500-I has been refined at 1.75 A resolution to an R factor of 20.9% and the structure of PH0500-II has been refined at 2.0 A resolution to an R factor of 23.4%. In both crystal forms as well as in solution the molecule appears to be a dimer. Searches of the databases for protein-fold similarities confirmed that the PH0500 protein is a PIN-domain protein with possible exonuclease activity and involvement in DNA or RNA editing.


==About this Structure==
Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii.,Jeyakanthan J, Inagaki E, Kuroishi C, Tahirov TH Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 May 1;61(Pt, 5):463-8. Epub 2005 Apr 26. PMID:16511069<ref>PMID:16511069</ref>
1V96 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 GOL as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1V96 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii., Jeyakanthan J, Inagaki E, Kuroishi C, Tahirov TH, Acta Crystallograph Sect F Struct Biol Cryst Commun. 2005 May 1;61(Pt, 5):463-8. Epub 2005 Apr 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16511069 16511069]
</div>
<div class="pdbe-citations 1v96" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
[[Category: Single protein]]
[[Category: Jeyakanthan J]]
[[Category: Jeyakanthan, J.]]
[[Category: Tahirov TH]]
[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
[[Category: Tahirov, T.H.]]
[[Category: GOL]]
[[Category: nucleotide binding protein]]
[[Category: riken structural genomics/proteomics initiative]]
[[Category: rossmann fold]]
[[Category: rsgi]]
[[Category: structural genomics]]
[[Category: trna synthetase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 21:53:27 2007''

Latest revision as of 23:59, 27 December 2023

Crystal structure of hypothetical protein of unknown function from pyrococcus horikoshii OT3

1v96, resolution 1.75Å

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