1l5y - Revision history

OCA at 09:10, 16 August 2023

OCA — Wed, 16 Aug 2023 09:10:03 GMT

←Older revision		Revision as of 09:10, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1l5y' size='340' side='right'caption='[[1l5y]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1l5y' size='340' side='right'caption='[[1l5y]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l5y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_9930 Atcc 9930~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L5Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l5y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L5Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=BF4:BERYLLIUM+TETRAFLUORIDE+ION'>BF4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.1Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qkk\|1qkk]], [[1l5z\|1l5z]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=BF4:BERYLLIUM+TETRAFLUORIDE+ION'>BF4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dctD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])~~</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=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [https://pdbe.org/1l5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [https://www.ebi.ac.uk/pdbsum/1l5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l5y 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=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [https://pdbe.org/1l5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [https://www.ebi.ac.uk/pdbsum/1l5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l5y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DCTD_RHIME DCTD_RHIME]] Member of the two-component regulatory system DctB/DctD involved in the transport of C4-dicarboxylates. When activated by DctB acts in conjunction with sigma-54 to activate the transcription of dctA.	+	[https://www.uniprot.org/uniprot/DCTD_RHIME DCTD_RHIME] Member of the two-component regulatory system DctB/DctD involved in the transport of C4-dicarboxylates. When activated by DctB acts in conjunction with sigma-54 to activate the transcription of dctA.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 9930]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jones~~, A D~~]]	+	[[Category: Sinorhizobium meliloti]]
-	[[Category: Meyer, M]]	+	[[Category: Jones AD]]
-	[[Category: Nixon~~, B T~~]]	+	[[Category: Meyer M]]
-	[[Category: Park, S]]	+	[[Category: Nixon BT]]
-	[[Category: Yennawar~~, H P~~]]	+	[[Category: Park S]]
-	[[Category: Yennawar~~, N H]]~~	+	[[Category: Yennawar HP]]
-	~~[[Category: Beryllofluoride bound two component receiver domain]]~~	+	[[Category: Yennawar NH]]
-	~~[[Category: Transcription regulator~~]]	+

OCA at 14:47, 27 October 2021

OCA — Wed, 27 Oct 2021 14:47:00 GMT

←Older revision		Revision as of 14:47, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1l5y' size='340' side='right'caption='[[1l5y]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1l5y' size='340' side='right'caption='[[1l5y]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l5y]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1L5Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l5y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L5Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=BF4:BERYLLIUM+TETRAFLUORIDE+ION'>BF4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=BF4:BERYLLIUM+TETRAFLUORIDE+ION'>BF4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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;'>[[1qkk\|1qkk]], [[1l5z\|1l5z]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qkk\|1qkk]], [[1l5z\|1l5z]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dctD ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dctD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [~~http~~://pdbe.org/1l5y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1l5y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1l5y 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=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [https://pdbe.org/1l5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [https://www.ebi.ac.uk/pdbsum/1l5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l5y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DCTD_RHIME DCTD_RHIME]] Member of the two-component regulatory system DctB/DctD involved in the transport of C4-dicarboxylates. When activated by DctB acts in conjunction with sigma-54 to activate the transcription of dctA.	+	[[https://www.uniprot.org/uniprot/DCTD_RHIME DCTD_RHIME]] Member of the two-component regulatory system DctB/DctD involved in the transport of C4-dicarboxylates. When activated by DctB acts in conjunction with sigma-54 to activate the transcription of dctA.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:55, 25 November 2020

OCA — Wed, 25 Nov 2020 07:55:26 GMT

←Older revision		Revision as of 07:55, 25 November 2020
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	==CRYSTAL STRUCTURE OF MG2+ / BEF3-BOUND RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD==		==CRYSTAL STRUCTURE OF MG2+ / BEF3-BOUND RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD==
-	<StructureSection load='1l5y' size='340' side='right' caption='[[1l5y]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1l5y' size='340' side='right'caption='[[1l5y]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l5y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1L5Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l5y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1L5Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=BF4:BERYLLIUM+TETRAFLUORIDE+ION'>BF4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=BF4:BERYLLIUM+TETRAFLUORIDE+ION'>BF4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qkk\|1qkk]], [[1l5z\|1l5z]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qkk\|1qkk]], [[1l5z\|1l5z]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dctD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dctD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</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=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [http://pdbe.org/1l5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [http://www.ebi.ac.uk/pdbsum/1l5y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l5y ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [http://pdbe.org/1l5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [http://www.ebi.ac.uk/pdbsum/1l5y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l5y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/l5/1l5y_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l5/1l5y_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>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 9930]]		[[Category: Atcc 9930]]
		+	[[Category: Large Structures]]
	[[Category: Jones, A D]]		[[Category: Jones, A D]]
	[[Category: Meyer, M]]		[[Category: Meyer, M]]

OCA at 07:24, 25 October 2017

OCA — Wed, 25 Oct 2017 07:24:09 GMT

←Older revision		Revision as of 07:24, 25 October 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF MG2+ / BEF3-BOUND RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD==		==CRYSTAL STRUCTURE OF MG2+ / BEF3-BOUND RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD==
	<StructureSection load='1l5y' size='340' side='right' caption='[[1l5y]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1l5y' size='340' side='right' caption='[[1l5y]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qkk\|1qkk]], [[1l5z\|1l5z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qkk\|1qkk]], [[1l5z\|1l5z]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dctD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dctD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</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=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [http://pdbe.org/1l5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [http://www.ebi.ac.uk/pdbsum/1l5y 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=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [http://pdbe.org/1l5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [http://www.ebi.ac.uk/pdbsum/1l5y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l5y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 02:07, 9 February 2016

OCA — Tue, 09 Feb 2016 02:07:27 GMT

←Older revision		Revision as of 02:07, 9 February 2016
Line 18:		Line 18:
	<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=1l5y ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:34, 10 September 2015

OCA — Thu, 10 Sep 2015 17:34:24 GMT

←Older revision		Revision as of 17:34, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1l5y' size='340' side='right' caption='[[1l5y]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1l5y' size='340' side='right' caption='[[1l5y]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l5y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sinorhizobium_meliloti Sinorhizobium meliloti~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L5Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l5y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L5Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=BF4:BERYLLIUM+TETRAFLUORIDE+ION'>BF4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=BF4:BERYLLIUM+TETRAFLUORIDE+ION'>BF4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qkk\|1qkk]], [[1l5z\|1l5z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qkk\|1qkk]], [[1l5z\|1l5z]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dctD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ~~Sinorhizobium meliloti~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dctD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</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=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [http://www.ebi.ac.uk/pdbsum/1l5y 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=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [http://pdbe.org/1l5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [http://www.ebi.ac.uk/pdbsum/1l5y PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1l5y" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sinorhizobium meliloti~~]]	+	[[Category: Atcc 9930]]
	[[Category: Jones, A D]]		[[Category: Jones, A D]]
	[[Category: Meyer, M]]		[[Category: Meyer, M]]

OCA at 03:41, 25 December 2014

OCA — Thu, 25 Dec 2014 03:41:15 GMT

←Older revision		Revision as of 03:41, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1l5y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L5Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[1l5y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L5Y FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=BF4:BERYLLIUM+TETRAFLUORIDE+ION'>BF4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=BF4:BERYLLIUM+TETRAFLUORIDE+ION'>BF4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qkk\|1qkk]], [[1l5z\|1l5z]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qkk\|1qkk]], [[1l5z\|1l5z]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dctD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 Sinorhizobium meliloti])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dctD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 Sinorhizobium meliloti])</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=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [http://www.ebi.ac.uk/pdbsum/1l5y 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=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [http://www.ebi.ac.uk/pdbsum/1l5y PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DCTD_RHIME DCTD_RHIME]] Member of the two-component regulatory system DctB/DctD involved in the transport of C4-dicarboxylates. When activated by DctB acts in conjunction with sigma-54 to activate the transcription of dctA.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]
-	[[Category: Jones, A D.]]	+	[[Category: Jones, A D]]
-	[[Category: Meyer, M.]]	+	[[Category: Meyer, M]]
-	[[Category: Nixon, B T.]]	+	[[Category: Nixon, B T]]
-	[[Category: Park, S.]]	+	[[Category: Park, S]]
-	[[Category: Yennawar, H P.]]	+	[[Category: Yennawar, H P]]
-	[[Category: Yennawar, N H.]]	+	[[Category: Yennawar, N H]]
	[[Category: Beryllofluoride bound two component receiver domain]]		[[Category: Beryllofluoride bound two component receiver domain]]
	[[Category: Transcription regulator]]		[[Category: Transcription regulator]]

OCA at 14:11, 28 September 2014

OCA — Sun, 28 Sep 2014 14:11:53 GMT

←Older revision		Revision as of 14:11, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1l5y.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF MG2+ / BEF3-BOUND RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD==
		+	<StructureSection load='1l5y' size='340' side='right' caption='[[1l5y]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1l5y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L5Y FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=BF4:BERYLLIUM+TETRAFLUORIDE+ION'>BF4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qkk\|1qkk]], [[1l5z\|1l5z]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dctD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 Sinorhizobium meliloti])</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=1l5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l5y RCSB], [http://www.ebi.ac.uk/pdbsum/1l5y 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/l5/1l5y_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 ==
		+	A Crystallogral structure is described for the Mg2+-BeF3--bound receiver domain of Sinorhizobium meliloti DctD bearing amino acid substitution E121K. Differences between the apo- and ligand-bound active sites are similar to those reported for other receiver domains. However, the off and on states of the DctD receiver domain are characterized by dramatically different dimeric structures, which supports the following hypothesis of signal transduction. In the off state, the receiver domain and coiled-coil linker form a dimer that inhibits oligomerization of the AAA+ ATPase domain. In this conformation, the receiver domain cannot be phosphorylated or bind Mg2+ and BeF3-. Instead, these modifications stabilize an alternative dimeric conformation that repositions the subunits by approximately 20 A, thus replacing the a4-b5-a5 interface with an a4-b5 interface. Reoriented receiver domains permit the ATPase domain to oligomerize and stimulate open complex formation by the s54 form of RNA polymerase. NtrC, which shares 38% sequence identity with DctD, works differently. Its activated receiver domain must facilitate oligomerization of its ATPase domain. Significant differences exist in the signaling surfaces of the DctD and NtrC receiver domains that may help explain how triggering the common two-component switch can variously regulate assembly of a AAA+ ATPase domain.

-	~~{{STRUCTURE_1l5y\| PDB=1l5y \| SCENE= }}~~	+	Two-component signaling in the AAA + ATPase DctD: binding Mg2+ and BeF3- selects between alternate dimeric states of the receiver domain.,Park S, Meyer M, Jones AD, Yennawar HP, Yennawar NH, Nixon BT FASEB J. 2002 Dec;16(14):1964-6. Epub 2002 Oct 4. PMID:12368235<ref>PMID:12368235</ref>

-	~~===CRYSTAL STRUCTURE OF MG2+~~ / ~~BEF3-BOUND RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12368235}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1l5y]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012368235<~~/~~ref~~><~~ref group="xtra">PMID:018557815</ref><references group="xtra"~~/>	+
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]
	[[Category: Jones, A D.]]		[[Category: Jones, A D.]]

OCA: Protected "1l5y" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 19:33:12 GMT

Protected "1l5y" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:33, 5 December 2012

OCA at 19:33, 5 December 2012

OCA — Wed, 05 Dec 2012 19:33:09 GMT

←Older revision		Revision as of 19:33, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1l5y.png\|left\|200px]]		[[Image:1l5y.png\|left\|200px]]

-	<!--
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-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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	{{STRUCTURE_1l5y\| PDB=1l5y \| SCENE= }}		{{STRUCTURE_1l5y\| PDB=1l5y \| SCENE= }}

	===CRYSTAL STRUCTURE OF MG2+ / BEF3-BOUND RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD===		===CRYSTAL STRUCTURE OF MG2+ / BEF3-BOUND RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12368235}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12368235 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_12368235}}		{{ABSTRACT_PUBMED_12368235}}

	==About this Structure==		==About this Structure==
-	~~1L5Y~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA].	+	[[1l5y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5Y OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12368235~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012368235</ref><ref group="xtra">PMID:018557815</ref><references group="xtra"/>
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]
	[[Category: Jones, A D.]]		[[Category: Jones, A D.]]
Line 32:		Line 20:
	[[Category: Yennawar, N H.]]		[[Category: Yennawar, N H.]]
	[[Category: Beryllofluoride bound two component receiver domain]]		[[Category: Beryllofluoride bound two component receiver domain]]
-		+	[[Category: Transcription regulator]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 05:36:01 2009''~~	+