2qq9 - Revision history

OCA at 11:38, 30 August 2023

OCA — Wed, 30 Aug 2023 11:38:26 GMT

←Older revision		Revision as of 11:38, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2qq9' size='340' side='right'caption='[[2qq9]], [[Resolution\|resolution]] 1.71Å' scene=''>		<StructureSection load='2qq9' size='340' side='right'caption='[[2qq9]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qq9]] 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=2QQ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QQ9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qq9]] 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=2QQ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QQ9 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]] 1.71Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1xcv\|1xcv]], [[1p92\|1p92]], [[1ddn\|1ddn]], [[2tdx\|2tdx]], [[2qqb\|2qqb]], [[2qqa\|2qqa]]~~</~~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">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=2qq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq9 OCA], [https://pdbe.org/2qq9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qq9 RCSB], [https://www.ebi.ac.uk/pdbsum/2qq9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qq9 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=2qq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq9 OCA], [https://pdbe.org/2qq9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qq9 RCSB], [https://www.ebi.ac.uk/pdbsum/2qq9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qq9 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]]
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	__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: Lattimer~~, J R~~]]	+	[[Category: Lattimer JR]]
-	[[Category: Ringe, D]]	+	[[Category: Ringe D]]
-	~~[[Category: Activation]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Dtxr]]~~	+
-	~~[[Category: Ferrous iron]]~~	+
-	~~[[Category: Helix-turn-helix]]~~	+
-	~~[[Category: Metal ion]]~~	+
-	~~[[Category: Regulator]]~~	+
-	~~[[Category: Repressor]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Transcription regulator~~]]	+

OCA at 08:29, 25 June 2021

OCA — Fri, 25 Jun 2021 08:29:08 GMT

←Older revision		Revision as of 08:29, 25 June 2021
Line 1:		Line 1:

	==Crystal Structure of DtxR(D6A C102D) Complexed with Nickel(II)==		==Crystal Structure of DtxR(D6A C102D) Complexed with Nickel(II)==
-	<StructureSection load='2qq9' size='340' side='right' caption='[[2qq9]], [[Resolution\|resolution]] 1.71Å' scene=''>	+	<StructureSection load='2qq9' size='340' side='right'caption='[[2qq9]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qq9]] 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=2QQ9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2QQ9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qq9]] 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=2QQ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QQ9 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">[[1xcv\|1xcv]], [[1p92\|1p92]], [[1ddn\|1ddn]], [[2tdx\|2tdx]], [[2qqb\|2qqb]], [[2qqa\|2qqa]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xcv\|1xcv]], [[1p92\|1p92]], [[1ddn\|1ddn]], [[2tdx\|2tdx]], [[2qqb\|2qqb]], [[2qqa\|2qqa]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">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">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=2qq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq9 OCA], [~~http~~://pdbe.org/2qq9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2qq9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2qq9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2qq9 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=2qq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq9 OCA], [https://pdbe.org/2qq9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qq9 RCSB], [https://www.ebi.ac.uk/pdbsum/2qq9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qq9 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]]
Line 38:		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 06:28, 4 April 2018

OCA — Wed, 04 Apr 2018 06:28:38 GMT

←Older revision		Revision as of 06:28, 4 April 2018
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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/qq/2qq9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qq/2qq9_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 2qq9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2qq9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Diphtheria toxin repressor\|Diphtheria toxin repressor]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:32, 25 October 2017

OCA — Wed, 25 Oct 2017 07:32:28 GMT

←Older revision		Revision as of 07:32, 25 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of DtxR(D6A C102D) Complexed with Nickel(II)==		==Crystal Structure of DtxR(D6A C102D) Complexed with Nickel(II)==
	<StructureSection load='2qq9' size='340' side='right' caption='[[2qq9]], [[Resolution\|resolution]] 1.71Å' scene=''>		<StructureSection load='2qq9' size='340' side='right' caption='[[2qq9]], [[Resolution\|resolution]] 1.71Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xcv\|1xcv]], [[1p92\|1p92]], [[1ddn\|1ddn]], [[2tdx\|2tdx]], [[2qqb\|2qqb]], [[2qqa\|2qqa]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xcv\|1xcv]], [[1p92\|1p92]], [[1ddn\|1ddn]], [[2tdx\|2tdx]], [[2qqb\|2qqb]], [[2qqa\|2qqa]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">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">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=2qq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq9 OCA], [http://pdbe.org/2qq9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qq9 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq9 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=2qq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq9 OCA], [http://pdbe.org/2qq9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qq9 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qq9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 2qq9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2qq9" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Diphtheria toxin repressor\|Diphtheria toxin repressor]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:57, 8 February 2016

OCA — Mon, 08 Feb 2016 13:57:18 GMT

←Older revision		Revision as of 13:57, 8 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=2qq9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:14, 10 September 2015

OCA — Thu, 10 Sep 2015 12:14:30 GMT

←Older revision		Revision as of 12:14, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2qq9' size='340' side='right' caption='[[2qq9]], [[Resolution\|resolution]] 1.71Å' scene=''>		<StructureSection load='2qq9' size='340' side='right' caption='[[2qq9]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qq9]] 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=2QQ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QQ9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qq9]] 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=2QQ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QQ9 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">[[1xcv\|1xcv]], [[1p92\|1p92]], [[1ddn\|1ddn]], [[2tdx\|2tdx]], [[2qqb\|2qqb]], [[2qqa\|2qqa]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xcv\|1xcv]], [[1p92\|1p92]], [[1ddn\|1ddn]], [[2tdx\|2tdx]], [[2qqb\|2qqb]], [[2qqa\|2qqa]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">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">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=2qq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qq9 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq9 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=2qq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq9 OCA], [http://pdbe.org/2qq9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qq9 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq9 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 2qq9" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__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 23:49, 24 December 2014

OCA — Wed, 24 Dec 2014 23:49:54 GMT

←Older revision		Revision as of 23:49, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2qq9]] 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=2QQ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QQ9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2qq9]] 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=2QQ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QQ9 FirstGlance]. <br>
-	</td></tr><tr><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><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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xcv\|1xcv]], [[1p92\|1p92]], [[1ddn\|1ddn]], [[2tdx\|2tdx]], [[2qqb\|2qqb]], [[2qqa\|2qqa]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xcv\|1xcv]], [[1p92\|1p92]], [[1ddn\|1ddn]], [[2tdx\|2tdx]], [[2qqb\|2qqb]], [[2qqa\|2qqa]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">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">dtxR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 Corynebacterium diphtheriae])</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=2qq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qq9 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq9 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=2qq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qq9 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq9 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]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[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: Lattimer, J R.]]	+	[[Category: Lattimer, J R]]
-	[[Category: Ringe, D.]]	+	[[Category: Ringe, D]]
	[[Category: Activation]]		[[Category: Activation]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]

OCA at 19:41, 30 September 2014

OCA — Tue, 30 Sep 2014 19:41:53 GMT

←Older revision		Revision as of 19:41, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2qq9.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of DtxR(D6A C102D) Complexed with Nickel(II)==
		+	<StructureSection load='2qq9' size='340' side='right' caption='[[2qq9]], [[Resolution\|resolution]] 1.71Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2qq9]] 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=2QQ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QQ9 FirstGlance]. <br>
		+	</td></tr><tr><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><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xcv\|1xcv]], [[1p92\|1p92]], [[1ddn\|1ddn]], [[2tdx\|2tdx]], [[2qqb\|2qqb]], [[2qqa\|2qqa]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dtxR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 Corynebacterium diphtheriae])</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=2qq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qq9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qq9 RCSB], [http://www.ebi.ac.uk/pdbsum/2qq9 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/qq/2qq9_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-regulated transcriptional repressor DtxR has been shown to repress the transcription of the diphtheria toxin and other genes associated with ferrous ion homeostasis in Corynebacterium diphtheriae. In vivo studies of single-alanine mutations located in the N-terminal helix of DtxR show that the activity of the mutants is reduced compared to that of the wild type. The three-dimensional structures of the apo and activated forms of DtxR show conformational changes in the N-terminal helix resulting from metal ion activation. We have studied the N-terminal helix mutants DtxR(D6A,C102D), DtxR(E9A,C102D), and DtxR(M10A,C102D) using crystallographic and calorimetric techniques to gain insight into the possible reasons for such behavior at a molecular level. The binding affinities for metal ion extracted from the calorimetric titrations of the mutants DtxR(D6A,C102D) and DtxR(E9A,C102D) are very similar to those found for DtxR(C102D), while the same experiments performed with the mutant DtxR(M10A,C102D), bearing the M10A mutation located in binding site 2, show a decreased binding affinity in a predictable fashion. These results suggest that the decreased activity observed in these mutants cannot be explained exclusively by changes in the binding affinity of the repressor. The crystal structures of Ni-DtxR(M10A,C102D), Ni-DtxR(E9A,C102D), and Ni-DtxR(D6A,C102D) clearly show the presence of two metal ions bound. In the structure of Ni-DtxR(M10A,C102D), a water replaces Met10 in binding site 2. In the structure of Ni-DtxR(D6A,C102D), the nonhelical conformation of the N-terminal region characteristic of the activated form is absent. The side chain of Asp6 is critical in stabilization of the nonhelical conformation. This conformation is identical in all high-resolution structures of activated DtxR with an intact N-terminal helix, suggesting relevance in DtxR's regulatory function.

-	~~{{STRUCTURE_2qq9\| PDB=2qq9 \| SCENE= }}~~	+	Role of the N-terminal helix in the metal ion-induced activation of the diphtheria toxin repressor DtxR.,D'Aquino JA, Lattimer JR, Denninger A, D'Aquino KE, Ringe D Biochemistry. 2007 Oct 23;46(42):11761-70. Epub 2007 Sep 29. PMID:17902703<ref>PMID:17902703</ref>

-	~~===Crystal Structure~~ of ~~DtxR(D6A C102D) Complexed with Nickel(II)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_17902703}}~~	+	==See Also==
-		+	*[[Diphtheria toxin repressor\|Diphtheria toxin repressor]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2qq9~~]] 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=2QQ9 OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:017902703<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Corynebacterium diphtheriae]]		[[Category: Corynebacterium diphtheriae]]
	[[Category: Aquino, J A.D.]]		[[Category: Aquino, J A.D.]]

OCA: Protected "2qq9" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 19:46:57 GMT

Protected "2qq9" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:46, 7 January 2013

OCA at 19:46, 7 January 2013

OCA — Mon, 07 Jan 2013 19:46:55 GMT

←Older revision		Revision as of 19:46, 7 January 2013
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-	{{Seed}}
	[[Image:2qq9.png\|left\|200px]]		[[Image:2qq9.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2qq9", 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.
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	{{STRUCTURE_2qq9\| PDB=2qq9 \| SCENE= }}		{{STRUCTURE_2qq9\| PDB=2qq9 \| SCENE= }}

	===Crystal Structure of DtxR(D6A C102D) Complexed with Nickel(II)===		===Crystal Structure of DtxR(D6A C102D) Complexed with Nickel(II)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17902703}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17902703 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17902703}}		{{ABSTRACT_PUBMED_17902703}}

	==About this Structure==		==About this Structure==
-	~~2QQ9~~ 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=2QQ9 OCA].	+	[[2qq9]] 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=2QQ9 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17902703~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017902703</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 42:		Line 29:
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
	[[Category: Transcription regulator]]		[[Category: Transcription regulator]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 23:12:46 2009''