3tcj - Revision history

OCA at 13:23, 14 March 2024

OCA — Thu, 14 Mar 2024 13:23:57 GMT

←Older revision		Revision as of 13:23, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3tcj' size='340' side='right'caption='[[3tcj]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='3tcj' size='340' side='right'caption='[[3tcj]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tcj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"achromobacter_fischeri"_(beijerinck_1889)_bergey_et_al._1930 "achromobacter~~ fischeri~~" (beijerinck 1889) bergey et al~~. ~~1930~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TCJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TCJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tcj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aliivibrio_fischeri Aliivibrio fischeri] and [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TCJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TCJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</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]] 1.93Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[3jrz\|3jrz]], [[3jsc\|3jsc]], [[3ku8\|3ku8]], [[3kua\|3kua]], [[3hpw\|3hpw]], [[3g7f\|3g7f]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">ccdB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=668 "Achromobacter fischeri" (Beijerinck 1889) Bergey et al. 1930])~~</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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [https://pdbe.org/3tcj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [https://www.ebi.ac.uk/pdbsum/3tcj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tcj 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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [https://pdbe.org/3tcj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [https://www.ebi.ac.uk/pdbsum/3tcj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tcj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~CCDA_ECO57 CCDA_ECO57~~]] Antitoxin component of a toxin-antitoxin (TA) module which inhibits the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Binds to and blocks the activity of CcdB; will also remove bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdB (By similarity).	+	[https://www.uniprot.org/uniprot/Q84B82_ALIFS Q84B82_ALIFS]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Intrinsically disordered proteins (IDPs) are proteins that lack a unique three-dimensional structure in their native state. Many have, however, been found to fold into a defined structure when interacting with specific binding partners. The energetic implications of such behavior have been widely discussed, yet experimental thermodynamic data is scarce. We present here a thorough thermodynamic and structural study of the binding of an IDP (antitoxin CcdA) to its molecular target (gyrase poison CcdB). We show that the binding-coupled folding of CcdA is driven by a combination of specific intramolecular interactions that favor the final folded structure and a less specific set of intermolecular contacts that provide a desolvation entropy boost. The folded structure of the bound IDP appears to be defined largely by its own amino acid sequence, with the binding partner functioning more as a facilitator than a mold to conform to. On the other hand, specific intermolecular interactions do increase the binding affinity up to the picomolar range. Overall, this study shows how an IDP can achieve very strong and structurally well-defined binding and it provides significant insight into the molecular forces that enable such binding properties.	+
-		+
-	Energetic basis of uncoupling folding from binding for an intrinsically disordered protein.,Drobnak I, De Jonge N, Haesaerts S, Vesnaver G, Loris R, Lah J J Am Chem Soc. 2013 Jan 30;135(4):1288-94. doi: 10.1021/ja305081b. Epub 2013 Jan , 16. PMID:23289531<ref>PMID:23289531</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3tcj" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aliivibrio fischeri]]
		+	[[Category: Escherichia coli O157:H7]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jonge, N De]]	+	[[Category: De Jonge N]]
-	[[Category: Loris, R]]	+	[[Category: Loris R]]
-	~~[[Category: Alpha+beta sh3 domain intrinsically disordered]]~~	+
-	~~[[Category: Toxin-antitoxin complex~~]]	+

OCA at 16:52, 6 July 2022

OCA — Wed, 06 Jul 2022 16:52:03 GMT

←Older revision		Revision as of 16:52, 6 July 2022
Line 1:		Line 1:

	==CcdB dimer from V. fisheri in complex with one C-terminal domain of F-plasmid CcdA==		==CcdB dimer from V. fisheri in complex with one C-terminal domain of F-plasmid CcdA==
-	<StructureSection load='3tcj' size='340' side='right' caption='[[3tcj]], [[Resolution\|resolution]] 1.93Å' scene=''>	+	<StructureSection load='3tcj' size='340' side='right'caption='[[3tcj]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tcj]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"achromobacter_fischeri"_(beijerinck_1889)_bergey_et_al._1930 "achromobacter fischeri" (beijerinck 1889) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TCJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TCJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tcj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"achromobacter_fischeri"_(beijerinck_1889)_bergey_et_al._1930 "achromobacter fischeri" (beijerinck 1889) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TCJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TCJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jrz\|3jrz]], [[3jsc\|3jsc]], [[3ku8\|3ku8]], [[3kua\|3kua]], [[3hpw\|3hpw]], [[3g7f\|3g7f]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3jrz\|3jrz]], [[3jsc\|3jsc]], [[3ku8\|3ku8]], [[3kua\|3kua]], [[3hpw\|3hpw]], [[3g7f\|3g7f]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccdB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=668 "Achromobacter fischeri" (Beijerinck 1889) Bergey et al. 1930])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccdB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=668 "Achromobacter fischeri" (Beijerinck 1889) Bergey et al. 1930])</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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [~~http~~://pdbe.org/3tcj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3tcj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3tcj 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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [https://pdbe.org/3tcj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [https://www.ebi.ac.uk/pdbsum/3tcj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tcj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CCDA_ECO57 CCDA_ECO57]] Antitoxin component of a toxin-antitoxin (TA) module which inhibits the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Binds to and blocks the activity of CcdB; will also remove bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdB (By similarity).	+	[[https://www.uniprot.org/uniprot/CCDA_ECO57 CCDA_ECO57]] Antitoxin component of a toxin-antitoxin (TA) module which inhibits the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Binds to and blocks the activity of CcdB; will also remove bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdB (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Jonge, N De]]		[[Category: Jonge, N De]]
	[[Category: Loris, R]]		[[Category: Loris, R]]
	[[Category: Alpha+beta sh3 domain intrinsically disordered]]		[[Category: Alpha+beta sh3 domain intrinsically disordered]]
	[[Category: Toxin-antitoxin complex]]		[[Category: Toxin-antitoxin complex]]

OCA at 04:44, 5 August 2016

OCA — Fri, 05 Aug 2016 04:44:09 GMT

←Older revision		Revision as of 04:44, 5 August 2016
Line 1:		Line 1:
		+
	==CcdB dimer from V. fisheri in complex with one C-terminal domain of F-plasmid CcdA==		==CcdB dimer from V. fisheri in complex with one C-terminal domain of F-plasmid CcdA==
	<StructureSection load='3tcj' size='340' side='right' caption='[[3tcj]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='3tcj' size='340' side='right' caption='[[3tcj]], [[Resolution\|resolution]] 1.93Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jrz\|3jrz]], [[3jsc\|3jsc]], [[3ku8\|3ku8]], [[3kua\|3kua]], [[3hpw\|3hpw]], [[3g7f\|3g7f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jrz\|3jrz]], [[3jsc\|3jsc]], [[3ku8\|3ku8]], [[3kua\|3kua]], [[3hpw\|3hpw]], [[3g7f\|3g7f]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=668 "Achromobacter fischeri" (Beijerinck 1889) Bergey et al. 1930])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=668 "Achromobacter fischeri" (Beijerinck 1889) Bergey et al. 1930])</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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [http://www.ebi.ac.uk/pdbsum/3tcj 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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [http://pdbe.org/3tcj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [http://www.ebi.ac.uk/pdbsum/3tcj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tcj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 3tcj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:53, 25 December 2014

OCA — Thu, 25 Dec 2014 15:53:04 GMT

←Older revision		Revision as of 15:53, 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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [http://www.ebi.ac.uk/pdbsum/3tcj 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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [http://www.ebi.ac.uk/pdbsum/3tcj PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CCDA_ECO57 CCDA_ECO57]] Antitoxin component of a toxin-antitoxin (TA) module which inhibits the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Binds to and blocks the activity of CcdB; will also remove bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdB (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Jonge, N De.]]	+	[[Category: Jonge, N De]]
-	[[Category: Loris, R.]]	+	[[Category: Loris, R]]
	[[Category: Alpha+beta sh3 domain intrinsically disordered]]		[[Category: Alpha+beta sh3 domain intrinsically disordered]]
	[[Category: Toxin-antitoxin complex]]		[[Category: Toxin-antitoxin complex]]

OCA at 08:35, 22 October 2014

OCA — Wed, 22 Oct 2014 08:35:18 GMT

←Older revision		Revision as of 08:35, 22 October 2014
Line 10:		Line 10:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~The ccd toxin-antitoxin module from the Escherichia coli F plasmid has a homologue on the Vibrio fischeri integron. The homologue of the toxin~~ (~~CcdB(Vfi~~)~~) was crystallized~~ in ~~two different crystal forms~~. ~~The first form belongs to space group I23 or I2(1)3~~, ~~with unit-cell parameter a = 84.5 A~~, ~~and diffracts~~ to ~~1.5 A resolution~~. The ~~second crystal form belongs to space group C2~~, ~~with unit-cell parameters~~ a ~~= 58.5, b = 43.6, c = 37.5 A, beta = 110.0 degrees,~~ and ~~diffracts to 1.7 A resolution. The complex~~ of ~~CcdB(Vfi) with~~ the ~~GyrA14(Vfi) fragment~~ of ~~V. fischeri gyrase crystallizes in space group P2~~(1)2(1)~~2(1), with unit~~-~~cell parameters~~ a ~~= 53.5, b = 94.6, c = 58.1 A,~~ and ~~diffracts to 2.2 A resolution~~. The ~~corresponding mixed complex with E. coli GyrA14(Ec) crystallizes in space group C2~~, with ~~unit-cell parameters~~ a ~~= 130~~.1, ~~b = 90.8, c = 58.1 A, beta = 102.6 degrees, and diffracts~~ to 1.~~95 A. Finally~~, ~~a complex between CcdB(Vfi)~~ and ~~part of the F~~-~~plasmid antitoxin CcdA(F) crystallizes in space group P2(1)2(1)2(1), with unit-cell parameters a = 46.9, b = 62.6, c = 82.0 A,~~ and ~~diffracts to 1.9 A resolution~~.	+	Intrinsically disordered proteins (IDPs) are proteins that lack a unique three-dimensional structure in their native state. Many have, however, been found to fold into a defined structure when interacting with specific binding partners. The energetic implications of such behavior have been widely discussed, yet experimental thermodynamic data is scarce. We present here a thorough thermodynamic and structural study of the binding of an IDP (antitoxin CcdA) to its molecular target (gyrase poison CcdB). We show that the binding-coupled folding of CcdA is driven by a combination of specific intramolecular interactions that favor the final folded structure and a less specific set of intermolecular contacts that provide a desolvation entropy boost. The folded structure of the bound IDP appears to be defined largely by its own amino acid sequence, with the binding partner functioning more as a facilitator than a mold to conform to. On the other hand, specific intermolecular interactions do increase the binding affinity up to the picomolar range. Overall, this study shows how an IDP can achieve very strong and structurally well-defined binding and it provides significant insight into the molecular forces that enable such binding properties.

-	~~Purification and crystallization~~ of ~~Vibrio fischeri CcdB and its complexes with fragments of gyrase and CcdA~~.,De Jonge N, ~~Buts L~~, ~~Vangelooven J, Mine N, Van Melderen L, Wyns L~~, Loris R ~~Acta Crystallogr Sect F Struct Biol Cryst Commun~~. ~~2007 Apr 1~~;63(~~Pt,~~ 4):~~356~~-60. Epub ~~2007 Mar 30~~. PMID:~~17401216~~<ref>PMID:~~17401216~~</ref>	+	Energetic basis of uncoupling folding from binding for an intrinsically disordered protein.,Drobnak I, De Jonge N, Haesaerts S, Vesnaver G, Loris R, Lah J J Am Chem Soc. 2013 Jan 30;135(4):1288-94. doi: 10.1021/ja305081b. Epub 2013 Jan , 16. PMID:23289531<ref>PMID:23289531</ref>

	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>

OCA at 05:43, 8 October 2014

OCA — Wed, 08 Oct 2014 05:43:20 GMT

←Older revision		Revision as of 05:43, 8 October 2014
Line 2:		Line 2:
	<StructureSection load='3tcj' size='340' side='right' caption='[[3tcj]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='3tcj' size='340' side='right' caption='[[3tcj]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tcj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aliivibrio_fischeri Aliivibrio~~ fischeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TCJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TCJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tcj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_fischeri"_(beijerinck_1889)_bergey_et_al._1930 "achromobacter fischeri" (beijerinck 1889) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TCJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TCJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jrz\|3jrz]], [[3jsc\|3jsc]], [[3ku8\|3ku8]], [[3kua\|3kua]], [[3hpw\|3hpw]], [[3g7f\|3g7f]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jrz\|3jrz]], [[3jsc\|3jsc]], [[3ku8\|3ku8]], [[3kua\|3kua]], [[3hpw\|3hpw]], [[3g7f\|3g7f]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=668 ~~Aliivibrio~~ fischeri])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=668 "Achromobacter fischeri" (Beijerinck 1889) Bergey et al. 1930])</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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [http://www.ebi.ac.uk/pdbsum/3tcj 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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [http://www.ebi.ac.uk/pdbsum/3tcj PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Aliivibrio fischeri]]~~	+	[[Category: Jonge, N De.]]
-	[[Category: Jonge, ~~Natalie~~ De.]]	+	[[Category: Loris, R.]]
-	[[Category: Loris, ~~Remy~~.]]	+
	[[Category: Alpha+beta sh3 domain intrinsically disordered]]		[[Category: Alpha+beta sh3 domain intrinsically disordered]]
	[[Category: Toxin-antitoxin complex]]		[[Category: Toxin-antitoxin complex]]

OCA at 09:12, 11 June 2014

OCA — Wed, 11 Jun 2014 09:12:39 GMT

←Older revision		Revision as of 09:12, 11 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3tcj.~~jpg~~\|~~left~~\|~~200px~~]]	+	==CcdB dimer from V. fisheri in complex with one C-terminal domain of F-plasmid CcdA==
		+	<StructureSection load='3tcj' size='340' side='right' caption='[[3tcj]], [[Resolution\|resolution]] 1.93Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3tcj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Aliivibrio_fischeri Aliivibrio fischeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TCJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TCJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jrz\|3jrz]], [[3jsc\|3jsc]], [[3ku8\|3ku8]], [[3kua\|3kua]], [[3hpw\|3hpw]], [[3g7f\|3g7f]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=668 Aliivibrio fischeri])</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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [http://www.ebi.ac.uk/pdbsum/3tcj PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The ccd toxin-antitoxin module from the Escherichia coli F plasmid has a homologue on the Vibrio fischeri integron. The homologue of the toxin (CcdB(Vfi)) was crystallized in two different crystal forms. The first form belongs to space group I23 or I2(1)3, with unit-cell parameter a = 84.5 A, and diffracts to 1.5 A resolution. The second crystal form belongs to space group C2, with unit-cell parameters a = 58.5, b = 43.6, c = 37.5 A, beta = 110.0 degrees, and diffracts to 1.7 A resolution. The complex of CcdB(Vfi) with the GyrA14(Vfi) fragment of V. fischeri gyrase crystallizes in space group P2(1)2(1)2(1), with unit-cell parameters a = 53.5, b = 94.6, c = 58.1 A, and diffracts to 2.2 A resolution. The corresponding mixed complex with E. coli GyrA14(Ec) crystallizes in space group C2, with unit-cell parameters a = 130.1, b = 90.8, c = 58.1 A, beta = 102.6 degrees, and diffracts to 1.95 A. Finally, a complex between CcdB(Vfi) and part of the F-plasmid antitoxin CcdA(F) crystallizes in space group P2(1)2(1)2(1), with unit-cell parameters a = 46.9, b = 62.6, c = 82.0 A, and diffracts to 1.9 A resolution.

-	~~{{STRUCTURE_3tcj\| PDB=3tcj \| SCENE= }}~~	+	Purification and crystallization of Vibrio fischeri CcdB and its complexes with fragments of gyrase and CcdA.,De Jonge N, Buts L, Vangelooven J, Mine N, Van Melderen L, Wyns L, Loris R Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Apr 1;63(Pt, 4):356-60. Epub 2007 Mar 30. PMID:17401216<ref>PMID:17401216</ref>

-	~~===CcdB dimer from V. fisheri in complex with one C-terminal domain~~ of ~~F-plasmid CcdA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17401216}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3tcj]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Aliivibrio_fischeri Aliivibrio fischeri]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3TCJ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017401216<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Aliivibrio fischeri]]		[[Category: Aliivibrio fischeri]]
	[[Category: Jonge, Natalie De.]]		[[Category: Jonge, Natalie De.]]

OCA at 05:48, 15 August 2012

OCA — Wed, 15 Aug 2012 05:48:35 GMT

←Older revision		Revision as of 05:48, 15 August 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3tcj.jpg\|left\|200px]]

-	~~The entry~~ 3tcj ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_3tcj\| PDB=3tcj \| SCENE= }}

-	~~Authors: Natalie De Jonge, Remy Loris~~	+	===CcdB dimer from V. fisheri in complex with one C-terminal domain of F-plasmid CcdA===

-	~~Description~~: ~~CcdB dimer~~ from V. ~~fisheri in complex with one C~~-~~terminal~~ domain ~~of F~~-~~plasmid CcdA~~	+	{{ABSTRACT_PUBMED_17401216}}
		+
		+	==About this Structure==
		+	[[3tcj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Aliivibrio_fischeri Aliivibrio fischeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TCJ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:017401216</ref><references group="xtra"/>
		+	[[Category: Aliivibrio fischeri]]
		+	[[Category: Jonge, Natalie De.]]
		+	[[Category: Loris, Remy.]]
		+	[[Category: Alpha+beta sh3 domain intrinsically disordered]]
		+	[[Category: Toxin-antitoxin complex]]

OCA at 06:22, 31 August 2011

OCA — Wed, 31 Aug 2011 06:22:54 GMT

←Older revision		Revision as of 06:22, 31 August 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3tcj is ON HOLD	+	The entry 3tcj is ON HOLD until Paper Publication

	Authors: Natalie De Jonge, Remy Loris		Authors: Natalie De Jonge, Remy Loris

	Description: CcdB dimer from V. fisheri in complex with one C-terminal domain of F-plasmid CcdA		Description: CcdB dimer from V. fisheri in complex with one C-terminal domain of F-plasmid CcdA

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

OCA — Wed, 17 Aug 2011 05:57:13 GMT

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

←Older revision

Revision as of 05:57, 17 August 2011