2ext - Revision history

OCA at 13:50, 13 March 2024

2024-03-13T13:50:19Z

← Older revision		Revision as of 13:50, 13 March 2024
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	<StructureSection load='2ext' size='340' side='right'caption='[[2ext]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2ext' size='340' side='right'caption='[[2ext]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ext]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXT FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ext]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXT FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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]] 1.8Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[2exs\|2exs]]~~<~~/div></td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">MTRB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])~~</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=2ext FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ext OCA], [https://pdbe.org/2ext PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ext RCSB], [https://www.ebi.ac.uk/pdbsum/2ext PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ext ProSAT]</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=2ext FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ext OCA], [https://pdbe.org/2ext PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ext RCSB], [https://www.ebi.ac.uk/pdbsum/2ext PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ext ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/MTRB_GEOSE MTRB_GEOSE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=2ext 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=2ext ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The protein TRAP (trp RNA binding attenuation protein) forms a highly thermostable ring-shaped 11-mer. By linking in tandem two, three, or four DNA sequences encoding TRAP monomers, we have engineered new rings that consist of 12 TRAP subunits and bind 12 ligand molecules. The hydrogen bonding pattern and buried surface area within and between subunits are essentially identical between the 11-mer and 12-mer crystal structures. Why do the artificial proteins choose to make single 12-mer rings? The 12-mer rings are highly sterically strained by their peptide linkers and far from thermostable. That proteins choose to adopt a strained conformation of few subunits rather than an unstrained one with 11 subunits demonstrates the importance of entropic factors in controlling protein-protein interactions in general.

	~~Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP.,Heddle JG, Yokoyama T, Yamashita I, Park SY, Tame JR Structure. 2006 May;14(5):925-33. PMID:16698553<ref>PMID:16698553</ref>~~

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2ext" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Tryptophan RNA-binding attenuation protein\|Tryptophan RNA-binding attenuation protein]]		*[[Tryptophan RNA-binding attenuation protein\|Tryptophan RNA-binding attenuation protein]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Atcc 12980~~]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Heddle~~, J G~~]]		[[Category: Heddle JG]]
	[[Category: Park~~, S Y~~]]		[[Category: Park SY]]
	[[Category: Tame~~, J R.H~~]]		[[Category: Tame JRH]]
	[[Category: Yamashita, I]]		[[Category: Yamashita I]]
	[[Category: Yokoyama, T]]		[[Category: Yokoyama T]]
	~~[[Category: 12-mer]]~~
	~~[[Category: Artificial]]~~
	~~[[Category: Engineered]]~~
	~~[[Category: Ring protein]]~~
	~~[[Category: Rna binding protein~~]]

OCA at 12:34, 10 February 2021

2021-02-10T12:34:16Z

← Older revision		Revision as of 12:34, 10 February 2021
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	==TRAP4 (engineered TRAP)==		==TRAP4 (engineered TRAP)==
	<StructureSection load='2ext' size='340' side='right' caption='[[2ext]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2ext' size='340' side='right'caption='[[2ext]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ext]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2EXT FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ext]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exs\|2exs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2exs\|2exs]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTRB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTRB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</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=2ext FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ext OCA], [~~http~~://pdbe.org/2ext PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ext RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ext PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ext ProSAT]</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=2ext FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ext OCA], [https://pdbe.org/2ext PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ext RCSB], [https://www.ebi.ac.uk/pdbsum/2ext PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ext ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 12980]]		[[Category: Atcc 12980]]
			[[Category: Large Structures]]
	[[Category: Heddle, J G]]		[[Category: Heddle, J G]]
	[[Category: Park, S Y]]		[[Category: Park, S Y]]

OCA at 09:15, 14 June 2018

2018-06-14T09:15:46Z

← Older revision		Revision as of 09:15, 14 June 2018
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	==TRAP4 (engineered TRAP)==		==TRAP4 (engineered TRAP)==
	<StructureSection load='2ext' size='340' side='right' caption='[[2ext]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2ext' size='340' side='right' caption='[[2ext]], [[Resolution\|resolution]] 1.80Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exs\|2exs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exs\|2exs]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</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=2ext FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ext OCA], [http://pdbe.org/2ext PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ext RCSB], [http://www.ebi.ac.uk/pdbsum/2ext PDBsum]</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=2ext FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ext OCA], [http://pdbe.org/2ext PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ext RCSB], [http://www.ebi.ac.uk/pdbsum/2ext PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ext ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ex/2ext_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ex/2ext_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>
	</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=2ext ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:59, 11 September 2015

2015-09-11T10:59:26Z

← Older revision		Revision as of 10:59, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2ext' size='340' side='right' caption='[[2ext]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2ext' size='340' side='right' caption='[[2ext]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ext]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_stearothermophilus Geobacillus stearothermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXT FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ext]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exs\|2exs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exs\|2exs]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ~~Geobacillus stearothermophilus~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</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=2ext FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ext OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ext RCSB], [http://www.ebi.ac.uk/pdbsum/2ext PDBsum]</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=2ext FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ext OCA], [http://pdbe.org/2ext PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ext RCSB], [http://www.ebi.ac.uk/pdbsum/2ext PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 2ext" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Geobacillus stearothermophilus~~]]		[[Category: Atcc 12980]]
	[[Category: Heddle, J G]]		[[Category: Heddle, J G]]
	[[Category: Park, S Y]]		[[Category: Park, S Y]]

OCA at 15:32, 25 December 2014

2014-12-25T15:32:40Z

← Older revision		Revision as of 15:32, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ext]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXT FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ext]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXT FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exs\|2exs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exs\|2exs]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</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=2ext FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ext OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ext RCSB], [http://www.ebi.ac.uk/pdbsum/2ext PDBsum]</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=2ext FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ext OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ext RCSB], [http://www.ebi.ac.uk/pdbsum/2ext PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Heddle, J G.]]		[[Category: Heddle, J G]]
	[[Category: Park, S Y.]]		[[Category: Park, S Y]]
	[[Category: Tame, J R.H.]]		[[Category: Tame, J R.H]]
	[[Category: Yamashita, I.]]		[[Category: Yamashita, I]]
	[[Category: Yokoyama, T.]]		[[Category: Yokoyama, T]]
	[[Category: 12-mer]]		[[Category: 12-mer]]
	[[Category: Artificial]]		[[Category: Artificial]]

OCA at 00:29, 30 September 2014

2014-09-30T00:29:08Z

← Older revision		Revision as of 00:29, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2ext~~.~~png~~\|~~left~~\|~~200px~~]]		==TRAP4 (engineered TRAP)==
			<StructureSection load='2ext' size='340' side='right' caption='[[2ext]], [[Resolution\|resolution]] 1.80Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2ext]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXT FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exs\|2exs]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</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=2ext FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ext OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ext RCSB], [http://www.ebi.ac.uk/pdbsum/2ext PDBsum]</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/ex/2ext_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 protein TRAP (trp RNA binding attenuation protein) forms a highly thermostable ring-shaped 11-mer. By linking in tandem two, three, or four DNA sequences encoding TRAP monomers, we have engineered new rings that consist of 12 TRAP subunits and bind 12 ligand molecules. The hydrogen bonding pattern and buried surface area within and between subunits are essentially identical between the 11-mer and 12-mer crystal structures. Why do the artificial proteins choose to make single 12-mer rings? The 12-mer rings are highly sterically strained by their peptide linkers and far from thermostable. That proteins choose to adopt a strained conformation of few subunits rather than an unstrained one with 11 subunits demonstrates the importance of entropic factors in controlling protein-protein interactions in general.

	~~{{STRUCTURE_2ext\| PDB=2ext \| SCENE= }}~~		Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP.,Heddle JG, Yokoyama T, Yamashita I, Park SY, Tame JR Structure. 2006 May;14(5):925-33. PMID:16698553<ref>PMID:16698553</ref>

	~~===TRAP4 (engineered TRAP)===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	~~{{ABSTRACT_PUBMED_16698553}}~~		==See Also==
			*[[Tryptophan RNA-binding attenuation protein\|Tryptophan RNA-binding attenuation protein]]
	==~~About this Structure~~==		== References ==
	[[~~2ext~~]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA].		<references/>
			__TOC__
	==~~Reference~~==		</StructureSection>
	<~~ref group="xtra">PMID:016698553<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Heddle, J G.]]		[[Category: Heddle, J G.]]

OCA: Protected "2ext" [edit=sysop:move=sysop]

2013-01-07T10:42:17Z

Protected "2ext" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:42, 7 January 2013
(No difference)

OCA at 10:42, 7 January 2013

2013-01-07T10:42:14Z

← Older revision		Revision as of 10:42, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2ext.png\|left\|200px]]		[[Image:2ext.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2ext", 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_2ext\| PDB=2ext \| SCENE= }}		{{STRUCTURE_2ext\| PDB=2ext \| SCENE= }}

	===TRAP4 (engineered TRAP)===		===TRAP4 (engineered TRAP)===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16698553}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16698553 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16698553}}		{{ABSTRACT_PUBMED_16698553}}

	==About this Structure==		==About this Structure==
	~~2EXT~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA].		[[2ext]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16698553~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016698553</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Heddle, J G.]]		[[Category: Heddle, J G.]]
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	[[Category: Engineered]]		[[Category: Engineered]]
	[[Category: Ring protein]]		[[Category: Ring protein]]
			[[Category: Rna binding protein]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 20:27:36 2009''~~

OCA at 18:27, 17 February 2009

2009-02-17T18:27:37Z

← Older revision		Revision as of 18:27, 17 February 2009
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	==About this Structure==		==About this Structure==
	2EXT is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA].		2EXT is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXT OCA].

	==Reference==		==Reference==
	~~Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP., Heddle JG, Yokoyama T, Yamashita I, Park SY, Tame JR, Structure. 2006 May;14(5):925-33.~~ PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~16698553 16698553]~~		<ref group="xtra">PMID:16698553</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	~~[[Category: Single protein]]~~
	[[Category: Heddle, J G.]]		[[Category: Heddle, J G.]]
	[[Category: Park, S Y.]]		[[Category: Park, S Y.]]
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	[[Category: Ring protein]]		[[Category: Ring protein]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 04~~:21:~~35 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:27:36 2009''

OCA at 01:21, 29 July 2008

2008-07-29T01:21:41Z

← Older revision		Revision as of 01:21, 29 July 2008
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	[[Image:2ext.~~gif~~\|left\|200px]]		{{Seed}}
			[[Image:2ext.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2ext\| PDB=2ext \| SCENE= }}		{{STRUCTURE_2ext\| PDB=2ext \| SCENE= }}

	~~'''~~TRAP4 (engineered TRAP)~~'''~~		===TRAP4 (engineered TRAP)===


	~~==Overview==~~		<!--
	The ~~protein TRAP~~ (~~trp RNA binding attenuation protein~~) ~~forms a highly thermostable ring-shaped 11-mer. By linking in tandem two~~, three, or four DNA sequences encoding TRAP monomers, we have engineered new rings that consist of 12 TRAP subunits and bind 12 ligand molecules. The hydrogen bonding pattern and buried surface area within and between subunits are essentially identical between the ~~11-mer and 12-mer crystal structures~~. ~~Why do the artificial proteins choose to make single 12~~-~~mer rings? The 12~~-mer rings are highly sterically strained by their peptide linkers and far from thermostable. That proteins choose to adopt a strained conformation of few subunits rather than an unstrained one with 11 subunits demonstrates the importance of entropic factors in controlling protein-protein interactions in general.		The line below this paragraph, {{ABSTRACT_PUBMED_16698553}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 16698553 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_16698553}}

	==About this Structure==		==About this Structure==
Line 31:		Line 35:
	[[Category: Engineered]]		[[Category: Engineered]]
	[[Category: Ring protein]]		[[Category: Ring protein]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 03~~:14:10 2008''
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 04:21:35 2008''