1wub - Revision history

OCA at 13:34, 13 March 2024

OCA — Wed, 13 Mar 2024 13:34:20 GMT

←Older revision		Revision as of 13:34, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='1wub' size='340' side='right'caption='[[1wub]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1wub' size='340' side='right'caption='[[1wub]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WUB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WUB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.65Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</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=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [https://pdbe.org/1wub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [https://www.ebi.ac.uk/pdbsum/1wub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wub ProSAT], [https://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></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=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [https://pdbe.org/1wub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [https://www.ebi.ac.uk/pdbsum/1wub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wub ProSAT], [https://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/P83815_THETH P83815_THETH]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 17:		Line 20:
	</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=1wub ConSurf].		</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=1wub ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The isoprenoid quinones exist widely among prokaryotes and eukaryotes. They play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. In the isoprenoid quinone biosynthetic pathway, polyprenyl pyrophosphates are used as isoprenoid side-chain precursors. Here we report the crystal structure of a novel polyprenyl pyrophosphate binding protein, TT1927b, from Thermus thermophilus HB8, complexed with its ligand. This protein belongs to the YceI-like family in the Pfam database, and its sequence homologs are present in a broad range of bacteria and archaea. The structure consists of an extended, eight-stranded, antiparallel beta-barrel. In the hydrophobic pore of the barrel, the protein binds the polyisoprenoid chain by hydrophobic interactions. Its overall structure resembles the lipocalin fold, but there is no sequence homology between TT1927b and the lipocalin family of proteins.
-
-	Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8.,Handa N, Terada T, Doi-Katayama Y, Hirota H, Tame JR, Park SY, Kuramitsu S, Shirouzu M, Yokoyama S Protein Sci. 2005 Apr;14(4):1004-10. Epub 2005 Mar 1. PMID:15741337<ref>PMID:15741337</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1wub" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Doi-Katayama, Y]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Hamana, H]]	+	[[Category: Doi-Katayama Y]]
-	[[Category: Handa, N]]	+	[[Category: Hamana H]]
-	[[Category: Hirota, H]]	+	[[Category: Handa N]]
-	[[Category: Idaka, M]]	+	[[Category: Hirota H]]
-	[[Category: Ishizuka, Y]]	+	[[Category: Idaka M]]
-	[[Category: Kuramitsu, S]]	+	[[Category: Ishizuka Y]]
-	[[Category: Park, S Y]]	+	[[Category: Kuramitsu S]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Park S-Y]]
-	[[Category: Shirouzu, M]]	+	[[Category: Shirouzu M]]
-	[[Category: Tame~~, J R.H~~]]	+	[[Category: Tame JRH]]
-	[[Category: Terada, T]]	+	[[Category: Terada T]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	~~[[Category: Beta-barrel]]~~	+
-	~~[[Category: Lipid binding protein]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 16:27, 27 October 2021

OCA — Wed, 27 Oct 2021 16:27:28 GMT

←Older revision		Revision as of 16:27, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1wub' size='340' side='right'caption='[[1wub]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1wub' size='340' side='right'caption='[[1wub]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WUB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WUB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [~~http~~://pdbe.org/1wub PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wub PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wub ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></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=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [https://pdbe.org/1wub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [https://www.ebi.ac.uk/pdbsum/1wub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wub ProSAT], [https://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 17:26, 22 January 2020

OCA — Wed, 22 Jan 2020 17:26:11 GMT

←Older revision		Revision as of 17:26, 22 January 2020
Line 1:		Line 1:

	==Crystal structure of the polyisoprenoid-binding protein, TT1927b, from Thermus thermophilus HB8==		==Crystal structure of the polyisoprenoid-binding protein, TT1927b, from Thermus thermophilus HB8==
-	<StructureSection load='1wub' size='340' side='right' caption='[[1wub]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='1wub' size='340' side='right'caption='[[1wub]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WUB FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WUB FirstGlance]. <br>
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
		+	[[Category: Large Structures]]
	[[Category: Doi-Katayama, Y]]		[[Category: Doi-Katayama, Y]]
	[[Category: Hamana, H]]		[[Category: Hamana, H]]

OCA at 16:12, 11 April 2018

OCA — Wed, 11 Apr 2018 16:12:28 GMT

←Older revision		Revision as of 16:12, 11 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of the polyisoprenoid-binding protein, TT1927b, from Thermus thermophilus HB8==		==Crystal structure of the polyisoprenoid-binding protein, TT1927b, from Thermus thermophilus HB8==
	<StructureSection load='1wub' size='340' side='right' caption='[[1wub]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1wub' size='340' side='right' caption='[[1wub]], [[Resolution\|resolution]] 1.65Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WUB FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WUB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [http://pdbe.org/1wub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [http://www.ebi.ac.uk/pdbsum/1wub PDBsum], [http://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [http://pdbe.org/1wub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [http://www.ebi.ac.uk/pdbsum/1wub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wub ProSAT], [http://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 10:		Line 11:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wu/1wub_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wu/1wub_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 14:45, 7 February 2016

OCA — Sun, 07 Feb 2016 14:45:05 GMT

←Older revision		Revision as of 14:45, 7 February 2016
Line 14:		Line 14:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=1wub ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:29, 10 September 2015

OCA — Thu, 10 Sep 2015 02:29:56 GMT

←Older revision		Revision as of 02:29, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1wub' size='340' side='right' caption='[[1wub]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1wub' size='340' side='right' caption='[[1wub]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WUB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WUB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [http://www.ebi.ac.uk/pdbsum/1wub PDBsum], [http://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [http://pdbe.org/1wub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [http://www.ebi.ac.uk/pdbsum/1wub PDBsum], [http://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 24:		Line 24:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1wub" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Doi-Katayama, Y]]		[[Category: Doi-Katayama, Y]]
	[[Category: Hamana, H]]		[[Category: Hamana, H]]

OCA at 12:35, 6 January 2015

OCA — Tue, 06 Jan 2015 12:35:25 GMT

←Older revision		Revision as of 12:35, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WUB FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WUB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [http://www.ebi.ac.uk/pdbsum/1wub PDBsum], [http://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [http://www.ebi.ac.uk/pdbsum/1wub PDBsum], [http://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Doi-Katayama, Y.]]	+	[[Category: Doi-Katayama, Y]]
-	[[Category: Hamana, H.]]	+	[[Category: Hamana, H]]
-	[[Category: Handa, N.]]	+	[[Category: Handa, N]]
-	[[Category: Hirota, H.]]	+	[[Category: Hirota, H]]
-	[[Category: Idaka, M.]]	+	[[Category: Idaka, M]]
-	[[Category: Ishizuka, Y.]]	+	[[Category: Ishizuka, Y]]
-	[[Category: Kuramitsu, S.]]	+	[[Category: Kuramitsu, S]]
-	[[Category: Park, S Y.]]	+	[[Category: Park, S Y]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Shirouzu, M.]]	+	[[Category: Shirouzu, M]]
-	[[Category: Tame, J R.H.]]	+	[[Category: Tame, J R.H]]
-	[[Category: Terada, T.]]	+	[[Category: Terada, T]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Beta-barrel]]		[[Category: Beta-barrel]]
	[[Category: Lipid binding protein]]		[[Category: Lipid binding protein]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 21:24, 29 September 2014

OCA — Mon, 29 Sep 2014 21:24:18 GMT

←Older revision		Revision as of 21:24, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1wub.~~png\|left~~\|200px]]	+	==Crystal structure of the polyisoprenoid-binding protein, TT1927b, from Thermus thermophilus HB8==
		+	<StructureSection load='1wub' size='340' side='right' caption='[[1wub]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1wub]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WUB FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OTP:(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL+TRIHYDROGEN+DIPHOSPHATE'>OTP</scene><br>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wub RCSB], [http://www.ebi.ac.uk/pdbsum/1wub PDBsum], [http://www.topsan.org/Proteins/RSGI/1wub TOPSAN]</span></td></tr>
		+	<table>
		+	== 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/wu/1wub_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The isoprenoid quinones exist widely among prokaryotes and eukaryotes. They play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. In the isoprenoid quinone biosynthetic pathway, polyprenyl pyrophosphates are used as isoprenoid side-chain precursors. Here we report the crystal structure of a novel polyprenyl pyrophosphate binding protein, TT1927b, from Thermus thermophilus HB8, complexed with its ligand. This protein belongs to the YceI-like family in the Pfam database, and its sequence homologs are present in a broad range of bacteria and archaea. The structure consists of an extended, eight-stranded, antiparallel beta-barrel. In the hydrophobic pore of the barrel, the protein binds the polyisoprenoid chain by hydrophobic interactions. Its overall structure resembles the lipocalin fold, but there is no sequence homology between TT1927b and the lipocalin family of proteins.

-	~~{{STRUCTURE_1wub\| PDB=1wub \| SCENE= }}~~	+	Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8.,Handa N, Terada T, Doi-Katayama Y, Hirota H, Tame JR, Park SY, Kuramitsu S, Shirouzu M, Yokoyama S Protein Sci. 2005 Apr;14(4):1004-10. Epub 2005 Mar 1. PMID:15741337<ref>PMID:15741337</ref>

-	~~===Crystal structure of the polyisoprenoid-binding protein~~, ~~TT1927b, from Thermus thermophilus HB8===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15741337}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1wub]] is~~ a ~~1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015741337<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Doi-Katayama, Y.]]		[[Category: Doi-Katayama, Y.]]

OCA: Protected "1wub" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 12:37:15 GMT

Protected "1wub" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:37, 5 January 2013

OCA at 12:37, 5 January 2013

OCA — Sat, 05 Jan 2013 12:37:13 GMT

←Older revision		Revision as of 12:37, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1wub.png\|left\|200px]]		[[Image:1wub.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1wub", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1wub\| PDB=1wub \| SCENE= }}		{{STRUCTURE_1wub\| PDB=1wub \| SCENE= }}

	===Crystal structure of the polyisoprenoid-binding protein, TT1927b, from Thermus thermophilus HB8===		===Crystal structure of the polyisoprenoid-binding protein, TT1927b, from Thermus thermophilus HB8===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15741337}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15741337 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15741337}}		{{ABSTRACT_PUBMED_15741337}}

	==About this Structure==		==About this Structure==
-	~~1WUB~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA].	+	[[1wub]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uf6 1uf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WUB OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15741337~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015741337</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Doi-Katayama, Y.]]		[[Category: Doi-Katayama, Y.]]
Line 39:		Line 27:
	[[Category: Yokoyama, S.]]		[[Category: Yokoyama, S.]]
	[[Category: Beta-barrel]]		[[Category: Beta-barrel]]
		+	[[Category: Lipid binding protein]]
	[[Category: Riken structural genomics/proteomics initiative]]		[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:32:59 2009''