3gh9 - Revision history

OCA at 15:39, 1 November 2023

OCA — Wed, 01 Nov 2023 15:39:39 GMT

←Older revision		Revision as of 15:39, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3gh9' size='340' side='right'caption='[[3gh9]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='3gh9' size='340' side='right'caption='[[3gh9]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gh9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GH9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gh9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GH9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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]] 1.69Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3eu3\|3eu3]], [[3eu4\|3eu4]], [[3gha\|3gha]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">bdbD, BSU33480, yvgV ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])~~</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=3gh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gh9 OCA], [https://pdbe.org/3gh9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gh9 RCSB], [https://www.ebi.ac.uk/pdbsum/3gh9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gh9 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=3gh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gh9 OCA], [https://pdbe.org/3gh9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gh9 RCSB], [https://www.ebi.ac.uk/pdbsum/3gh9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gh9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BDBD_BACSU BDBD_BACSU]] Required for the stabilization, possibly via formation of a disulfide bond, of the obligatory competence protein ComGC. May be required for the stability of secreted proteins with disulfide bonds. Not required for sporulation.<ref>PMID:11744713</ref>	+	[https://www.uniprot.org/uniprot/BDBD_BACSU BDBD_BACSU] Required for the stabilization, possibly via formation of a disulfide bond, of the obligatory competence protein ComGC. May be required for the stability of secreted proteins with disulfide bonds. Not required for sporulation.<ref>PMID:11744713</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 31:

	==See Also==		==See Also==
-	*[[Protein disulfide oxidoreductase\|Protein disulfide oxidoreductase]]	+	*[[Protein disulfide oxidoreductase 3D structures\|Protein disulfide oxidoreductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Crow, A]]	+	[[Category: Crow A]]
-	[[Category: Hederstedt, L]]	+	[[Category: Hederstedt L]]
-	[[Category: Le-Brun~~, N E~~]]	+	[[Category: Le-Brun NE]]
-	[[Category: Lewin, A]]	+	[[Category: Lewin A]]
-	~~[[Category: Bdbd]]~~	+
-	~~[[Category: Competence]]~~	+
-	~~[[Category: Disulfide bond]]~~	+
-	~~[[Category: Dsba]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Redox-active center]]~~	+
-	~~[[Category: Trx-like~~]]	+

OCA at 08:05, 9 March 2022

OCA — Wed, 09 Mar 2022 08:05:18 GMT

←Older revision		Revision as of 08:05, 9 March 2022
Line 1:		Line 1:

	==Crystal structure of EDTA-treated BdbD (Oxidised)==		==Crystal structure of EDTA-treated BdbD (Oxidised)==
-	<StructureSection load='3gh9' size='340' side='right' caption='[[3gh9]], [[Resolution\|resolution]] 1.69Å' scene=''>	+	<StructureSection load='3gh9' size='340' side='right'caption='[[3gh9]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gh9]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GH9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gh9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GH9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eu3\|3eu3]], [[3eu4\|3eu4]], [[3gha\|3gha]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3eu3\|3eu3]], [[3eu4\|3eu4]], [[3gha\|3gha]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bdbD, BSU33480, yvgV ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bdbD, BSU33480, yvgV ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3gh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gh9 OCA], [~~http~~://pdbe.org/3gh9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3gh9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3gh9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3gh9 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=3gh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gh9 OCA], [https://pdbe.org/3gh9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gh9 RCSB], [https://www.ebi.ac.uk/pdbsum/3gh9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gh9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BDBD_BACSU BDBD_BACSU]] Required for the stabilization, possibly via formation of a disulfide bond, of the obligatory competence protein ComGC. May be required for the stability of secreted proteins with disulfide bonds. Not required for sporulation.<ref>PMID:11744713</ref>	+	[[https://www.uniprot.org/uniprot/BDBD_BACSU BDBD_BACSU]] Required for the stabilization, possibly via formation of a disulfide bond, of the obligatory competence protein ComGC. May be required for the stability of secreted proteins with disulfide bonds. Not required for sporulation.<ref>PMID:11744713</ref>
	== 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: Vibrio subtilis ehrenberg 1835]]		[[Category: Vibrio subtilis ehrenberg 1835]]
		+	[[Category: Large Structures]]
	[[Category: Crow, A]]		[[Category: Crow, A]]
	[[Category: Hederstedt, L]]		[[Category: Hederstedt, L]]

OCA at 05:44, 7 December 2018

OCA — Fri, 07 Dec 2018 05:44:42 GMT

←Older revision		Revision as of 05:44, 7 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of EDTA-treated BdbD (Oxidised)==		==Crystal structure of EDTA-treated BdbD (Oxidised)==
	<StructureSection load='3gh9' size='340' side='right' caption='[[3gh9]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='3gh9' size='340' side='right' caption='[[3gh9]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gh9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"~~bacillus_globigii~~"~~_migula_1900~~ "~~bacillus globigii~~" ~~migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GH9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gh9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GH9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eu3\|3eu3]], [[3eu4\|3eu4]], [[3gha\|3gha]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eu3\|3eu3]], [[3eu4\|3eu4]], [[3gha\|3gha]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bdbD, BSU33480, yvgV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "~~Bacillus globigii~~" ~~Migula 1900~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bdbD, BSU33480, yvgV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3gh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gh9 OCA], [http://pdbe.org/3gh9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gh9 RCSB], [http://www.ebi.ac.uk/pdbsum/3gh9 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=3gh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gh9 OCA], [http://pdbe.org/3gh9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gh9 RCSB], [http://www.ebi.ac.uk/pdbsum/3gh9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gh9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gh/3gh9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gh/3gh9_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 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Crow, A]]		[[Category: Crow, A]]
	[[Category: Hederstedt, L]]		[[Category: Hederstedt, L]]

OCA at 05:03, 10 February 2016

OCA — Wed, 10 Feb 2016 05:03:11 GMT

←Older revision		Revision as of 05:03, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='3gh9' size='340' side='right' caption='[[3gh9]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='3gh9' size='340' side='right' caption='[[3gh9]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gh9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GH9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gh9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GH9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eu3\|3eu3]], [[3eu4\|3eu4]], [[3gha\|3gha]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eu3\|3eu3]], [[3eu4\|3eu4]], [[3gha\|3gha]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bdbD, BSU33480, yvgV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bdbD, BSU33480, yvgV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=3gh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gh9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gh9 RCSB], [http://www.ebi.ac.uk/pdbsum/3gh9 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=3gh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gh9 OCA], [http://pdbe.org/3gh9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gh9 RCSB], [http://www.ebi.ac.uk/pdbsum/3gh9 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=3gh9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3gh9" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Crow, A]]		[[Category: Crow, A]]
	[[Category: Hederstedt, L]]		[[Category: Hederstedt, L]]

OCA at 11:58, 25 December 2014

OCA — Thu, 25 Dec 2014 11:58:03 GMT

←Older revision		Revision as of 11:58, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3gh9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GH9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3gh9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GH9 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eu3\|3eu3]], [[3eu4\|3eu4]], [[3gha\|3gha]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eu3\|3eu3]], [[3eu4\|3eu4]], [[3gha\|3gha]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bdbD, BSU33480, yvgV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bdbD, BSU33480, yvgV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=3gh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gh9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gh9 RCSB], [http://www.ebi.ac.uk/pdbsum/3gh9 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=3gh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gh9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gh9 RCSB], [http://www.ebi.ac.uk/pdbsum/3gh9 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BDBD_BACSU BDBD_BACSU]] Required for the stabilization, possibly via formation of a disulfide bond, of the obligatory competence protein ComGC. May be required for the stability of secreted proteins with disulfide bonds. Not required for sporulation.<ref>PMID:11744713</ref>
	== 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: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
-	[[Category: Crow, A.]]	+	[[Category: Crow, A]]
-	[[Category: Hederstedt, L.]]	+	[[Category: Hederstedt, L]]
-	[[Category: Le-Brun, N E.]]	+	[[Category: Le-Brun, N E]]
-	[[Category: Lewin, A.]]	+	[[Category: Lewin, A]]
	[[Category: Bdbd]]		[[Category: Bdbd]]
	[[Category: Competence]]		[[Category: Competence]]

OCA at 13:17, 29 September 2014

OCA — Mon, 29 Sep 2014 13:17:31 GMT

←Older revision		Revision as of 13:17, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3gh9.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of EDTA-treated BdbD (Oxidised)==
		+	<StructureSection load='3gh9' size='340' side='right' caption='[[3gh9]], [[Resolution\|resolution]] 1.69Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3gh9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GH9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eu3\|3eu3]], [[3eu4\|3eu4]], [[3gha\|3gha]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bdbD, BSU33480, yvgV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=3gh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gh9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gh9 RCSB], [http://www.ebi.ac.uk/pdbsum/3gh9 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/gh/3gh9_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 ==
		+	BdbD is a thiol:disulfide oxidoreductase (TDOR) from Bacillus subtilis that functions to introduce disulfide bonds in substrate proteins/peptides on the outside of the cytoplasmic membrane and, as such, plays a key role in disulfide bond management. Here we demonstrate that the protein is membrane-associated in B. subtilis and present the crystal structure of the soluble part of the protein lacking its membrane anchor. This reveals that BdbD is similar in structure to Escherichia coli DsbA, with a thioredoxin-like domain with an inserted helical domain. A major difference, however, is the presence in BdbD of a metal site, fully occupied by Ca(2+), at an inter-domain position some 14 A away from the CXXC active site. The midpoint reduction potential of soluble BdbD was determined as -75 mV versus normal hydrogen electrode, and the active site N-terminal cysteine thiol was shown to have a low pK(a), consistent with BdbD being an oxidizing TDOR. Equilibrium unfolding studies revealed that the oxidizing power of the protein is based on the instability introduced by the disulfide bond in the oxidized form. The crystal structure of Ca(2+)-depleted BdbD showed that the protein remained folded, with only minor conformational changes. However, the reduced form of Ca(2+)-depleted BdbD was significantly less stable than reduced Ca(2+)-containing protein, and the midpoint reduction potential was shifted by approximately -20 mV, suggesting that Ca(2+) functions to boost the oxidizing power of the protein. Finally, we demonstrate that electron exchange does not occur between BdbD and B. subtilis ResA, a low potential extra-cytoplasmic TDOR.

-	~~{{STRUCTURE_3gh9\| PDB=3gh9 \| SCENE= }}~~	+	Crystal structure and biophysical properties of Bacillus subtilis BdbD. An oxidizing thiol:disulfide oxidoreductase containing a novel metal site.,Crow A, Lewin A, Hecht O, Carlsson Moller M, Moore GR, Hederstedt L, Le Brun NE J Biol Chem. 2009 Aug 28;284(35):23719-33. Epub 2009 Jun 17. PMID:19535335<ref>PMID:19535335</ref>

-	~~===Crystal structure~~ of ~~EDTA-treated BdbD (Oxidised)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19535335}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3gh9]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_subtilis Bacillus subtilis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA].~~	+

	==See Also==		==See Also==
	*[[Protein disulfide oxidoreductase\|Protein disulfide oxidoreductase]]		*[[Protein disulfide oxidoreductase\|Protein disulfide oxidoreductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019535335<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Crow, A.]]		[[Category: Crow, A.]]

OCA at 16:25, 20 October 2012

OCA — Sat, 20 Oct 2012 16:25:28 GMT

←Older revision		Revision as of 16:25, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3gh9]] is a 1 chain structure ~~of [[Protein disulfide oxidoreductase]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA].	+	[[3gh9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA].

	==See Also==		==See Also==

OCA: Protected "3gh9" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 21:38:48 GMT

Protected "3gh9" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:38, 26 July 2012

OCA at 21:38, 26 July 2012

OCA — Thu, 26 Jul 2012 21:38:47 GMT

←Older revision		Revision as of 21:38, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3gh9.png\|left\|200px]]		[[Image:3gh9.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3gh9", 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_3gh9\| PDB=3gh9 \| SCENE= }}		{{STRUCTURE_3gh9\| PDB=3gh9 \| SCENE= }}

	===Crystal structure of EDTA-treated BdbD (Oxidised)===		===Crystal structure of EDTA-treated BdbD (Oxidised)===

		+	{{ABSTRACT_PUBMED_19535335}}

	==About this Structure==		==About this Structure==
-	~~3GH9~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA].	+	[[3gh9]] is a 1 chain structure of [[Protein disulfide oxidoreductase]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA].
		+
		+	==See Also==
		+	*[[Protein disulfide oxidoreductase\|Protein disulfide oxidoreductase]]
		+
		+	==Reference==
		+	<ref group="xtra">PMID:019535335</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Crow, A.]]		[[Category: Crow, A.]]
Line 27:		Line 27:
	[[Category: Redox-active center]]		[[Category: Redox-active center]]
	[[Category: Trx-like]]		[[Category: Trx-like]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 9 20:13:42 2009''

OCA at 17:06, 9 September 2009

OCA — Wed, 09 Sep 2009 17:06:26 GMT

←Older revision		Revision as of 17:06, 9 September 2009
Line 12:		Line 12:
	===Crystal structure of EDTA-treated BdbD (Oxidised)===		===Crystal structure of EDTA-treated BdbD (Oxidised)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19535335}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19535335 is the PubMed ID number.
-	-->
-	{{ABSTRACT_PUBMED_19535335}}

	==About this Structure==		==About this Structure==
	3GH9 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA].		3GH9 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH9 OCA].
-
-	==Reference==
-	<ref group="xtra">PMID:19535335</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Crow, A.]]		[[Category: Crow, A.]]
Line 37:		Line 28:
	[[Category: Trx-like]]		[[Category: Trx-like]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 9 08:39:41 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 9 20:13:42 2009''