This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1v96

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

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

Structural highlights

1v96 is a 2 chain structure with sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.75Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

VAPC4_PYRHO Toxic component of a toxin-antitoxin (TA) module. An RNase.[HAMAP-Rule:MF_00265]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Jeyakanthan J, Inagaki E, Kuroishi C, Tahirov TH. Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 May 1;61(Pt, 5):463-8. Epub 2005 Apr 26. PMID:16511069 doi:10.1107/S1744309105012406

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1v96"

Categories: Large Structures | Pyrococcus horikoshii | Jeyakanthan J | Tahirov TH

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1v96.png|left|200px]]
-<!--
+==Crystal structure of hypothetical protein of unknown function from pyrococcus horikoshii OT3==
-The line below this paragraph, containing "STRUCTURE_1v96", creates the "Structure Box" on the page.
+<StructureSection load='1v96' size='340' side='right'caption='[[1v96]], [[Resolution|resolution]] 1.75&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'>[[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>
-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]] 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>
-{{STRUCTURE_1v96|  PDB=1v96  |  SCENE=  }}
+<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.
-===Crystal structure of hypothetical protein of unknown function from pyrococcus horikoshii OT3===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16511069}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1v96" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16511069 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16511069}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-V96 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=1V96 OCA].
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/16511069 16511069]
 [[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: Nucleotide binding protein]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rossmann fold]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-[[Category: Trna synthetase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 07:57:03 2008''

1v96

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox