3glx - Revision history

OCA at 07:07, 6 September 2023

OCA — Wed, 06 Sep 2023 07:07:57 GMT

←Older revision		Revision as of 07:07, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3glx' size='340' side='right'caption='[[3glx]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3glx' size='340' side='right'caption='[[3glx]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3glx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus~~ diphtheriae~~" kruse in flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GLX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3glx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GLX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.85Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2qqa\|2qqa]], [[2qqb\|2qqb]], [[2qq9\|2qq9]], [[1ddn\|1ddn]], [[1p92\|1p92]], [[1xcv\|1xcv]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">DIP1414, dtxR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])~~</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=3glx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glx OCA], [https://pdbe.org/3glx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3glx RCSB], [https://www.ebi.ac.uk/pdbsum/3glx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3glx 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=3glx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glx OCA], [https://pdbe.org/3glx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3glx RCSB], [https://www.ebi.ac.uk/pdbsum/3glx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3glx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI]] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.	+	[https://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ diphtheriae ~~kruse in flugge 1886~~]]	+	[[Category: Corynebacterium diphtheriae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aquino~~, J A.D~~]]	+	[[Category: D'Aquino JA]]
-	[[Category: Aquino~~, K E.D~~]]	+	[[Category: D'Aquino KE]]
-	[[Category: Denninger, A]]	+	[[Category: Denninger A]]
-	[[Category: Moulin, A]]	+	[[Category: Moulin A]]
-	[[Category: Ringe, D]]	+	[[Category: Ringe D]]
-	~~[[Category: Activation]]~~	+
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Dtxr]]~~	+
-	~~[[Category: Ferrous iron]]~~	+
-	~~[[Category: Helix-turn-helix]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Metal ion]]~~	+
-	~~[[Category: Regulator]]~~	+
-	~~[[Category: Repressor]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Transcriptional regulation]]~~	+
-	~~[[Category: Transcriptional regulator~~]]	+

OCA at 20:08, 20 October 2021

OCA — Wed, 20 Oct 2021 20:08:01 GMT

←Older revision		Revision as of 20:08, 20 October 2021
Line 1:		Line 1:

	==Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II)==		==Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II)==
-	<StructureSection load='3glx' size='340' side='right' caption='[[3glx]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='3glx' size='340' side='right'caption='[[3glx]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3glx]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus diphtheriae" kruse in flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GLX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3glx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus diphtheriae" kruse in flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GLX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qqa\|2qqa]], [[2qqb\|2qqb]], [[2qq9\|2qq9]], [[1ddn\|1ddn]], [[1p92\|1p92]], [[1xcv\|1xcv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2qqa\|2qqa]], [[2qqb\|2qqb]], [[2qq9\|2qq9]], [[1ddn\|1ddn]], [[1p92\|1p92]], [[1xcv\|1xcv]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DIP1414, dtxR ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DIP1414, dtxR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])</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=3glx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glx OCA], [~~http~~://pdbe.org/3glx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3glx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3glx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3glx 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=3glx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glx OCA], [https://pdbe.org/3glx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3glx RCSB], [https://www.ebi.ac.uk/pdbsum/3glx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3glx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI]] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.	+	[[https://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI]] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gl/3glx_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gl/3glx_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 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 3glx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3glx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Diphtheria toxin repressor\|Diphtheria toxin repressor]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus diphtheriae kruse in flugge 1886]]		[[Category: Bacillus diphtheriae kruse in flugge 1886]]
		+	[[Category: Large Structures]]
	[[Category: Aquino, J A.D]]		[[Category: Aquino, J A.D]]
	[[Category: Aquino, K E.D]]		[[Category: Aquino, K E.D]]

OCA at 07:07, 1 November 2017

OCA — Wed, 01 Nov 2017 07:07:13 GMT

←Older revision		Revision as of 07:07, 1 November 2017
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 3glx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3glx" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Diphtheria toxin repressor\|Diphtheria toxin repressor]]
	== References ==		== References ==
	<references/>		<references/>
Line 44:		Line 41:
	[[Category: Ringe, D]]		[[Category: Ringe, D]]
	[[Category: Activation]]		[[Category: Activation]]
		+	[[Category: Cytoplasm]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
	[[Category: Dtxr]]		[[Category: Dtxr]]

OCA at 09:56, 5 August 2016

OCA — Fri, 05 Aug 2016 09:56:27 GMT

←Older revision		Revision as of 09:56, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II)==		==Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II)==
	<StructureSection load='3glx' size='340' side='right' caption='[[3glx]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3glx' size='340' side='right' caption='[[3glx]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3glx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Corynebacterium_diphtheriae Corynebacterium~~ diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GLX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3glx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus diphtheriae" kruse in flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GLX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qqa\|2qqa]], [[2qqb\|2qqb]], [[2qq9\|2qq9]], [[1ddn\|1ddn]], [[1p92\|1p92]], [[1xcv\|1xcv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qqa\|2qqa]], [[2qqb\|2qqb]], [[2qq9\|2qq9]], [[1ddn\|1ddn]], [[1p92\|1p92]], [[1xcv\|1xcv]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DIP1414, dtxR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 ~~Corynebacterium~~ diphtheriae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DIP1414, dtxR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])</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=3glx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3glx RCSB], [http://www.ebi.ac.uk/pdbsum/3glx 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=3glx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glx OCA], [http://pdbe.org/3glx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3glx RCSB], [http://www.ebi.ac.uk/pdbsum/3glx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3glx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=3glx ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	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 3glx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Corynebacterium~~ diphtheriae]]	+	[[Category: Bacillus diphtheriae kruse in flugge 1886]]
	[[Category: Aquino, J A.D]]		[[Category: Aquino, J A.D]]
	[[Category: Aquino, K E.D]]		[[Category: Aquino, K E.D]]

OCA at 17:52, 25 December 2014

OCA — Thu, 25 Dec 2014 17:52:00 GMT

←Older revision		Revision as of 17:52, 25 December 2014
Line 8:		Line 8:
	<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=3glx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3glx RCSB], [http://www.ebi.ac.uk/pdbsum/3glx 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=3glx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3glx RCSB], [http://www.ebi.ac.uk/pdbsum/3glx PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI]] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:20, 8 December 2014

OCA — Mon, 08 Dec 2014 09:20:06 GMT

←Older revision		Revision as of 09:20, 8 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3glx.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II)==
		+	<StructureSection load='3glx' size='340' side='right' caption='[[3glx]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3glx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GLX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qqa\|2qqa]], [[2qqb\|2qqb]], [[2qq9\|2qq9]], [[1ddn\|1ddn]], [[1p92\|1p92]], [[1xcv\|1xcv]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DIP1414, dtxR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 Corynebacterium diphtheriae])</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=3glx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3glx RCSB], [http://www.ebi.ac.uk/pdbsum/3glx 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/gl/3glx_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 metal-ion-activated diphtheria toxin repressor (DtxR) is responsible for the regulation of virulence and other genes in Corynebacterium diphtheriae. A single point mutation in DtxR, DtxR(E175K), causes this mutant repressor to have a hyperactive phenotype. Mice infected with Mycobacterium tuberculosis transformed with plasmids carrying this mutant gene show reduced signs of the tuberculosis infection. Corynebacterial DtxR is able to complement mycobacterial IdeR and vice versa. To date, an explanation for the hyperactivity of DtxR(E175K) has remained elusive. In an attempt to address this issue, we have solved the first crystal structure of DtxR(E175K) and characterized this mutant using circular dichroism, isothermal titration calorimetry, and other biochemical techniques. The results show that although DtxR(E175K) and the wild type have similar secondary structures, DtxR(E175K) gains additional thermostability upon activation with metal ions, which may lead to this mutant requiring a lower concentration of metal ions to reach the same levels of thermostability as the wild-type protein. The E175K mutation causes binding site 1 to retain metal ion bound at all times, which can only be removed by incubation with an ion chelator. The crystal structure of DtxR(E175K) shows an empty binding site 2 without evidence of oxidation of Cys102. The association constant for this low-affinity binding site of DtxR(E175K) obtained from calorimetric titration with Ni(II) is K(a)=7.6+/-0.5x10(4), which is very similar to the reported value for the wild-type repressor, K(a)=6.3x10(4). Both the wild type and DtxR(E175K) require the same amount of metal ion to produce a shift in the electrophoretic mobility shift assay, but unlike the wild type, DtxR(E175K) binding to its cognate DNA [tox promoter-operator (toxPO)] does not require metal-ion supplementation in the running buffer. In the timescale of these experiments, the Mn(II)-DtxR(E175K)-toxPO complex is insensitive to changes in the environmental cation concentrations. In addition to Mn(II), Ni(II), Co(II), Cd(II), and Zn(II) are able to sustain the hyperactive phenotype. These results demonstrate a prominent role of binding site 1 in the activation of DtxR and support the hypothesis that DtxR(E175K) attenuates the expression of virulence due to the decreased ability of the Me(II)-DtxR(E175K)-toxPO complex to dissociate at low concentrations of metal ions.

-	~~{{STRUCTURE_3glx\| PDB=3glx \| SCENE= }}~~	+	Decreased sensitivity to changes in the concentration of metal ions as the basis for the hyperactivity of DtxR(E175K).,D'Aquino JA, Denninger AR, Moulin AG, D'Aquino KE, Ringe D J Mol Biol. 2009 Jul 3;390(1):112-23. Epub 2009 May 8. PMID:19433095<ref>PMID:19433095</ref>

-	~~===Crystal Structure Analysis~~ of the ~~DtxR(E175K) complexed with Ni(II)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_19433095}}~~	+	==See Also==
-		+	*[[Diphtheria toxin repressor\|Diphtheria toxin repressor]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3glx~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLX OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:019433095<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Corynebacterium diphtheriae]]		[[Category: Corynebacterium diphtheriae]]
-	[[Category: Aquino, J A.D.]]	+	[[Category: Aquino, J A.D]]
-	[[Category: Aquino, K E.D.]]	+	[[Category: Aquino, K E.D]]
-	[[Category: Denninger, A.]]	+	[[Category: Denninger, A]]
-	[[Category: Moulin, A.]]	+	[[Category: Moulin, A]]
-	[[Category: Ringe, D.]]	+	[[Category: Ringe, D]]
	[[Category: Activation]]		[[Category: Activation]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]

OCA: Protected "3glx" [edit=sysop:move=sysop]

OCA — Wed, 27 Feb 2013 15:17:19 GMT

Protected "3glx" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:17, 27 February 2013

OCA at 15:17, 27 February 2013

OCA — Wed, 27 Feb 2013 15:17:16 GMT

←Older revision		Revision as of 15:17, 27 February 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3glx.png\|left\|200px]]		[[Image:3glx.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3glx", 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_3glx\| PDB=3glx \| SCENE= }}		{{STRUCTURE_3glx\| PDB=3glx \| SCENE= }}

	===Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II)===		===Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19433095}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19433095 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19433095}}		{{ABSTRACT_PUBMED_19433095}}

	==About this Structure==		==About this Structure==
-	~~3GLX~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLX OCA].	+	[[3glx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLX OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19433095~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019433095</ref><references group="xtra"/>
	[[Category: Corynebacterium diphtheriae]]		[[Category: Corynebacterium diphtheriae]]
	[[Category: Aquino, J A.D.]]		[[Category: Aquino, J A.D.]]
Line 31:		Line 19:
	[[Category: Ringe, D.]]		[[Category: Ringe, D.]]
	[[Category: Activation]]		[[Category: Activation]]
-	[[Category: Cytoplasm]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
	[[Category: Dtxr]]		[[Category: Dtxr]]
Line 44:		Line 31:
	[[Category: Transcriptional regulation]]		[[Category: Transcriptional regulation]]
	[[Category: Transcriptional regulator]]		[[Category: Transcriptional regulator]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 8 12:55:42 2009''

OCA at 09:55, 8 July 2009

OCA — Wed, 08 Jul 2009 09:55:45 GMT

←Older revision		Revision as of 09:55, 8 July 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3glx.~~jpg~~\|left\|200px]]	+	[[Image:3glx.png\|left\|200px]]

	<!--		<!--
Line 45:		Line 45:
	[[Category: Transcriptional regulator]]		[[Category: Transcriptional regulator]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 10 18~~:05:26 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 8 12:55:42 2009''

OCA at 15:05, 10 June 2009

OCA — Wed, 10 Jun 2009 15:05:27 GMT

←Older revision		Revision as of 15:05, 10 June 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3glx.jpg\|left\|200px]]

-	The ~~entry 3glx~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3glx", 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_3glx\| PDB=3glx \| SCENE= }}

-	~~Authors: D'Aquino, J.A., Denninger, A., Moulin, A., D'Aquino, K.E., Ringe, D.~~	+	===Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II)===

-	Description: Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II)

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~May 13 09~~:32:41 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19433095}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19433095 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19433095}}
		+
		+	==About this Structure==
		+	3GLX is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLX OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19433095</ref><references group="xtra"/>
		+	[[Category: Corynebacterium diphtheriae]]
		+	[[Category: Aquino, J A.D.]]
		+	[[Category: Aquino, K E.D.]]
		+	[[Category: Denninger, A.]]
		+	[[Category: Moulin, A.]]
		+	[[Category: Ringe, D.]]
		+	[[Category: Activation]]
		+	[[Category: Cytoplasm]]
		+	[[Category: Dna-binding]]
		+	[[Category: Dtxr]]
		+	[[Category: Ferrous iron]]
		+	[[Category: Helix-turn-helix]]
		+	[[Category: Iron]]
		+	[[Category: Metal ion]]
		+	[[Category: Regulator]]
		+	[[Category: Repressor]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]
		+	[[Category: Transcriptional regulation]]
		+	[[Category: Transcriptional regulator]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 10 18:05:26 2009''