2dkf - Revision history

OCA at 07:51, 23 October 2024

2024-10-23T07:51:18Z

← Older revision		Revision as of 07:51, 23 October 2024
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	<StructureSection load='2dkf' size='340' side='right'caption='[[2dkf]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2dkf' size='340' side='right'caption='[[2dkf]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thet8 Thet8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKF FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.8Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[2az4\|2az4]]~~</~~div></td></tr>~~
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat"~~>~~TTHA0252 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])~~</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=2dkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkf OCA], [https://pdbe.org/2dkf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkf RCSB], [https://www.ebi.ac.uk/pdbsum/2dkf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkf ProSAT], [https://www.topsan.org/Proteins/RSGI/2dkf 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=2dkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkf OCA], [https://pdbe.org/2dkf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkf RCSB], [https://www.ebi.ac.uk/pdbsum/2dkf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkf ProSAT], [https://www.topsan.org/Proteins/RSGI/2dkf TOPSAN]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/RNSE_THET8 RNSE_THET8] Has endoribonuclease activity towards 23S and 16S rRNA (in vitro).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkf_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkf_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Thet8~~]]		[[Category: Thermus thermophilus HB8]]
	[[Category: Ishikawa, I]]		[[Category: Ishikawa I]]
	[[Category: Kuramitsu, S]]		[[Category: Kuramitsu S]]
	[[Category: Masui, R]]		[[Category: Masui R]]
	[[Category: Nakagawa, N]]		[[Category: Nakagawa N]]
	~~[[Category: Structural genomic~~]]		[[Category: Yokoyama S]]
	[[Category: Yokoyama, S]]
	~~[[Category: Beta-casp family]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Metallo-beta-lactamase]]~~
	~~[[Category: National project on protein structural and functional analyse]]~~
	~~[[Category: Nppsfa]]~~
	~~[[Category: Ribonuclease]]~~
	~~[[Category: Rnase e]]~~
	~~[[Category: Rsgi]]~~
	~~[[Category: Thermus thermophilus~~]]

OCA at 12:05, 3 February 2021

2021-02-03T12:05:40Z

← Older revision		Revision as of 12:05, 3 February 2021
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	==Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily==		==Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily==
	<StructureSection load='2dkf' size='340' side='right' caption='[[2dkf]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2dkf' size='340' side='right'caption='[[2dkf]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkf]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DKF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2az4\|2az4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2az4\|2az4]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0252 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0252 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=2dkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkf OCA], [~~http~~://pdbe.org/2dkf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dkf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dkf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkf ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2dkf 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=2dkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkf OCA], [https://pdbe.org/2dkf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkf RCSB], [https://www.ebi.ac.uk/pdbsum/2dkf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkf ProSAT], [https://www.topsan.org/Proteins/RSGI/2dkf TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
	*[[Beta-lactamase\|Beta-lactamase]]		*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Thet8]]		[[Category: Thet8]]
	[[Category: Ishikawa, I]]		[[Category: Ishikawa, I]]

OCA at 06:26, 30 May 2018

2018-05-30T06:26:31Z

← Older revision		Revision as of 06:26, 30 May 2018
Line 1:		Line 1:

	==Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily==		==Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily==
	<StructureSection load='2dkf' size='340' side='right' caption='[[2dkf]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2dkf' size='340' side='right' caption='[[2dkf]], [[Resolution\|resolution]] 2.80Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2az4\|2az4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2az4\|2az4]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0252 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0252 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=2dkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkf OCA], [http://pdbe.org/2dkf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dkf RCSB], [http://www.ebi.ac.uk/pdbsum/2dkf PDBsum], [http://www.topsan.org/Proteins/RSGI/2dkf 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=2dkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkf OCA], [http://pdbe.org/2dkf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dkf RCSB], [http://www.ebi.ac.uk/pdbsum/2dkf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkf ProSAT], [http://www.topsan.org/Proteins/RSGI/2dkf TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkf_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkf_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=2dkf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:46, 11 September 2015

2015-09-11T16:46:37Z

← Older revision		Revision as of 16:46, 11 September 2015
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	<StructureSection load='2dkf' size='340' side='right' caption='[[2dkf]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2dkf' size='340' side='right' caption='[[2dkf]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus_hb8 Thermus thermophilus hb8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2az4\|2az4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2az4\|2az4]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0252 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 ~~Thermus thermophilus HB8~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0252 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=2dkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkf RCSB], [http://www.ebi.ac.uk/pdbsum/2dkf PDBsum], [http://www.topsan.org/Proteins/RSGI/2dkf 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=2dkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkf OCA], [http://pdbe.org/2dkf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dkf RCSB], [http://www.ebi.ac.uk/pdbsum/2dkf PDBsum], [http://www.topsan.org/Proteins/RSGI/2dkf TOPSAN]</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 2dkf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Thermus thermophilus hb8~~]]		[[Category: Thet8]]
	[[Category: Ishikawa, I]]		[[Category: Ishikawa, I]]
	[[Category: Kuramitsu, S]]		[[Category: Kuramitsu, S]]

OCA at 16:32, 15 January 2015

2015-01-15T16:32:29Z

← Older revision		Revision as of 16:32, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKF FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2az4\|2az4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2az4\|2az4]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0252 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 Thermus thermophilus HB8])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0252 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 Thermus thermophilus HB8])</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=2dkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkf RCSB], [http://www.ebi.ac.uk/pdbsum/2dkf PDBsum], [http://www.topsan.org/Proteins/RSGI/2dkf 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=2dkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkf RCSB], [http://www.ebi.ac.uk/pdbsum/2dkf PDBsum], [http://www.topsan.org/Proteins/RSGI/2dkf 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 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus hb8]]		[[Category: Thermus thermophilus hb8]]
	[[Category: Ishikawa, I.]]		[[Category: Ishikawa, I]]
	[[Category: Kuramitsu, S.]]		[[Category: Kuramitsu, S]]
	[[Category: Masui, R.]]		[[Category: Masui, R]]
	[[Category: Nakagawa, N.]]		[[Category: Nakagawa, N]]
	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]		[[Category: Structural genomic]]
	[[Category: Yokoyama, S.]]		[[Category: Yokoyama, S]]
	[[Category: Beta-casp family]]		[[Category: Beta-casp family]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
Line 47:		Line 47:
	[[Category: Nppsfa]]		[[Category: Nppsfa]]
	[[Category: Ribonuclease]]		[[Category: Ribonuclease]]
	~~[[Category: Riken structural genomics/proteomics initiative]]~~
	[[Category: Rnase e]]		[[Category: Rnase e]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
	~~[[Category: Structural genomic]]~~
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA at 02:21, 29 September 2014

2014-09-29T02:21:05Z

← Older revision		Revision as of 02:21, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2dkf~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily==
			<StructureSection load='2dkf' size='340' side='right' caption='[[2dkf]], [[Resolution\|resolution]] 2.80Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dkf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKF FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
			<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2az4\|2az4]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0252 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 Thermus thermophilus HB8])</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=2dkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkf RCSB], [http://www.ebi.ac.uk/pdbsum/2dkf PDBsum], [http://www.topsan.org/Proteins/RSGI/2dkf 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/dk/2dkf_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 ==
			In bacterial RNA metabolism, mRNA degradation is an important process for gene expression. Recently, a novel ribonuclease (RNase), belonging to the beta-CASP family within the metallo-beta-lactamase superfamily, was identified as a functional homologue of RNase E, a major component for mRNA degradation in Escherichia coli. Here, we have determined the crystal structure of TTHA0252 from Thermus thermophilus HB8, which represents the first report of the tertiary structure of a beta-CASP family protein. TTHA0252 comprises two separate domains: a metallo-beta-lactamase domain and a "clamp" domain. The active site of the enzyme is located in a cleft between the two domains, which includes two zinc ions coordinated by seven conserved residues. Although this configuration is similar to those of other beta-lactamases, TTHA0252 has one conserved His residue characteristic of the beta-CASP family as a ligand. We also detected nuclease activity of TTHA0252 against rRNAs of T. thermophilus. Our results reveal structural and functional aspects of novel RNase E-like enzymes with a beta-CASP fold.

	~~{{STRUCTURE_2dkf\| PDB=2dkf \| SCENE= }}~~		Crystal structure of TTHA0252 from Thermus thermophilus HB8, a RNA degradation protein of the metallo-beta-lactamase superfamily.,Ishikawa H, Nakagawa N, Kuramitsu S, Masui R J Biochem. 2006 Oct;140(4):535-42. Epub 2006 Aug 31. PMID:16945939<ref>PMID:16945939</ref>

	~~===Crystal Structure of TTHA0252 from Thermus thermophilus HB8~~, a ~~RNA Degradation Protein~~ of the ~~Metallo-beta-lactamase Superfamily===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16945939}}~~

	~~==About this Structure==~~
	~~[[2dkf]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]~~. ~~Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=2DKF OCA].~~

	==See Also==		==See Also==
	*[[Beta-lactamase\|Beta-lactamase]]		*[[Beta-lactamase\|Beta-lactamase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:016945939<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Thermus thermophilus hb8]]		[[Category: Thermus thermophilus hb8]]
	[[Category: Ishikawa, I.]]		[[Category: Ishikawa, I.]]

OCA at 20:24, 20 October 2012

2012-10-20T20:24:37Z

← Older revision		Revision as of 20:24, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2dkf]] is a 4 chain structure ~~of [[Beta-lactamase]]~~ with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus~~ Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA].		[[2dkf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA].

	==See Also==		==See Also==
Line 15:		Line 15:
	==Reference==		==Reference==
	<ref group="xtra">PMID:016945939</ref><references group="xtra"/>		<ref group="xtra">PMID:016945939</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus hb8]]
	[[Category: Ishikawa, I.]]		[[Category: Ishikawa, I.]]
	[[Category: Kuramitsu, S.]]		[[Category: Kuramitsu, S.]]

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

2012-07-27T10:23:30Z

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

← Older revision	Revision as of 10:23, 27 July 2012
(No difference)

OCA at 10:23, 27 July 2012

2012-07-27T10:23:28Z

← Older revision		Revision as of 10:23, 27 July 2012
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	~~{{Seed}}~~
	[[Image:2dkf.png\|left\|200px]]		[[Image:2dkf.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2dkf", 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_2dkf\| PDB=2dkf \| SCENE= }}		{{STRUCTURE_2dkf\| PDB=2dkf \| SCENE= }}

	===Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily===		===Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16945939}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16945939 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16945939}}		{{ABSTRACT_PUBMED_16945939}}

	==About this Structure==		==About this Structure==
	~~2DKF~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA].		[[2dkf]] is a 4 chain structure of [[Beta-lactamase]] with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA].

			==See Also==
			*[[Beta-lactamase\|Beta-lactamase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16945939~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016945939</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Ishikawa, I.]]		[[Category: Ishikawa, I.]]
Line 32:		Line 23:
	[[Category: Yokoyama, S.]]		[[Category: Yokoyama, S.]]
	[[Category: Beta-casp family]]		[[Category: Beta-casp family]]
			[[Category: Hydrolase]]
	[[Category: Metallo-beta-lactamase]]		[[Category: Metallo-beta-lactamase]]
	[[Category: National project on protein structural and functional analyse]]		[[Category: National project on protein structural and functional analyse]]
Line 41:		Line 33:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:07:02 2009''~~

OCA at 02:07, 18 February 2009

2009-02-18T02:07:02Z

← Older revision		Revision as of 02:07, 18 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
	Crystal structure of TTHA0252 from Thermus thermophilus HB8, a RNA degradation protein of the metallo-beta-lactamase superfamily., Ishikawa H, Nakagawa N, Kuramitsu S, Masui R, J Biochem. 2006 Oct;140(4):535-42. Epub 2006 Aug 31. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16945939 16945939]~~		<ref group="xtra">PMID:16945939</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Ishikawa, I.]]		[[Category: Ishikawa, I.]]
Line 42:		Line 42:
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16 10~~:02~~:04 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:07:02 2009''