5clv - Revision history

OCA at 11:21, 10 January 2024

OCA — Wed, 10 Jan 2024 11:21:08 GMT

←Older revision		Revision as of 11:21, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5clv]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CLV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CLV FirstGlance]. <br>		<table><tr><td colspan='2'>[[5clv]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CLV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CLV FirstGlance]. <br>
-	</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=5clv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5clv OCA], [https://pdbe.org/5clv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5clv RCSB], [https://www.ebi.ac.uk/pdbsum/5clv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5clv ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.5Å</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=5clv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5clv OCA], [https://pdbe.org/5clv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5clv RCSB], [https://www.ebi.ac.uk/pdbsum/5clv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5clv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 12:14, 14 June 2023

OCA — Wed, 14 Jun 2023 12:14:19 GMT

←Older revision		Revision as of 12:14, 14 June 2023
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	<StructureSection load='5clv' size='340' side='right'caption='[[5clv]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5clv' size='340' side='right'caption='[[5clv]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5clv]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CLV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CLV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5clv]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CLV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CLV FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ckt\|5ckt]]</td></tr>~~	+	</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=5clv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5clv OCA], [https://pdbe.org/5clv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5clv RCSB], [https://www.ebi.ac.uk/pdbsum/5clv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5clv ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trfB, korA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=5clv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5clv OCA], [~~http~~://pdbe.org/5clv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5clv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5clv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5clv ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KORA2_ECOLX KORA2_ECOLX]] In conjunction with KorB, inhibits the transcription of kilA, trfA and korAB operons. In conjunction with KorC is responsible for the negative control of kilC and kilE operons.	+	[https://www.uniprot.org/uniprot/KORA2_ECOLX KORA2_ECOLX] In conjunction with KorB, inhibits the transcription of kilA, trfA and korAB operons. In conjunction with KorC is responsible for the negative control of kilC and kilE operons.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hyde~~, E I~~]]	+	[[Category: Hyde EI]]
-	[[Category: Rajasekar~~, K V~~]]	+	[[Category: Rajasekar KV]]
-	[[Category: White~~, S A]]~~	+	[[Category: White SA]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Helix-turn-helix]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 11:44, 27 March 2020

OCA — Fri, 27 Mar 2020 11:44:22 GMT

←Older revision		Revision as of 11:44, 27 March 2020
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	==Crystal Structure of KorA-operator DNA complex (KorA-OA)==		==Crystal Structure of KorA-operator DNA complex (KorA-OA)==
-	<StructureSection load='5clv' size='340' side='right' caption='[[5clv]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5clv' size='340' side='right'caption='[[5clv]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5clv]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CLV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CLV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5clv]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CLV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CLV FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ckt\|5ckt]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ckt\|5ckt]]</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=5clv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5clv OCA], [http://pdbe.org/5clv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5clv RCSB], [http://www.ebi.ac.uk/pdbsum/5clv PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trfB, korA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=5clv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5clv OCA], [http://pdbe.org/5clv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5clv RCSB], [http://www.ebi.ac.uk/pdbsum/5clv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5clv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Hyde, E I]]		[[Category: Hyde, E I]]
	[[Category: Rajasekar, K V]]		[[Category: Rajasekar, K V]]

OCA at 04:05, 12 May 2016

OCA — Thu, 12 May 2016 04:05:45 GMT

←Older revision		Revision as of 04:05, 12 May 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5clv is ~~ON HOLD~~	+	==Crystal Structure of KorA-operator DNA complex (KorA-OA)==
		+	<StructureSection load='5clv' size='340' side='right' caption='[[5clv]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5clv]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CLV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CLV FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ckt\|5ckt]]</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=5clv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5clv OCA], [http://pdbe.org/5clv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5clv RCSB], [http://www.ebi.ac.uk/pdbsum/5clv PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KORA2_ECOLX KORA2_ECOLX]] In conjunction with KorB, inhibits the transcription of kilA, trfA and korAB operons. In conjunction with KorC is responsible for the negative control of kilC and kilE operons.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The IncP (Incompatibility group P) plasmids are important carriers in the spread of antibiotic resistance across Gram-negative bacteria. Gene expression in the IncP-1 plasmids is stringently controlled by a network of four global repressors, KorA, KorB, TrbA and KorC interacting cooperatively. Intriguingly, KorA and KorB can act as co-repressors at varying distances between their operators, even when they are moved to be on opposite sides of the DNA. KorA is a homodimer with the 101-amino acid subunits, folding into an N-terminal DNA-binding domain and a C-terminal dimerization domain. In this study, we have determined the structures of the free KorA repressor and two complexes each bound to a 20-bp palindromic DNA duplex containing its consensus operator sequence. Using a combination of X-ray crystallography, nuclear magnetic resonance spectroscopy, SAXS and molecular dynamics calculations, we show that the linker between the two domains is very flexible and the protein remains highly mobile in the presence of DNA. This flexibility allows the DNA-binding domains of the dimer to straddle the operator DNA on binding and is likely to be important in cooperative binding to KorB. Unexpectedly, the C-terminal domain of KorA is structurally similar to the dimerization domain of the tumour suppressor p53.

-	~~Authors: White~~, ~~S.A.~~, ~~Hyde~~, ~~E.I~~., Rajasekar, K.V.	+	Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator.,Rajasekar KV, Lovering AL, Dancea F, Scott DJ, Harris SA, Bingle LE, Roessle M, Thomas CM, Hyde EI, White SA Nucleic Acids Res. 2016 Mar 25. pii: gkw191. PMID:27016739<ref>PMID:27016739</ref>

-	~~Description: Crystal Structure~~ of ~~KorA~~-~~operator DNA complex (KorA~~-~~OA)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Rajasekar, K.V]]	+	<div class="pdbe-citations 5clv" style="background-color:#fffaf0;"></div>
-	[[Category: White, S.A]]	+	== References ==
-	[[Category: ~~Hyde, E.I~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hyde, E I]]
		+	[[Category: Rajasekar, K V]]
		+	[[Category: White, S A]]
		+	[[Category: Complex]]
		+	[[Category: Helix-turn-helix]]
		+	[[Category: Transcription]]

OCA: Protected "5clv" [edit=sysop:move=sysop]

OCA — Wed, 22 Jul 2015 13:19:18 GMT

Protected "5clv" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:19, 22 July 2015

OCA: New page: '''Unreleased structure''' The entry 5clv is ON HOLD Authors: White, S.A., Hyde, E.I., Rajasekar, K.V. Description: Crystal Structure of KorA-operator DNA complex (KorA-OA) [[Category:...

OCA — Wed, 22 Jul 2015 13:19:17 GMT

New page: '''Unreleased structure''' The entry 5clv is ON HOLD Authors: White, S.A., Hyde, E.I., Rajasekar, K.V. Description: Crystal Structure of KorA-operator DNA complex (KorA-OA) [[Category:...

New page

'''Unreleased structure'''

The entry 5clv is ON HOLD

Authors: White, S.A., Hyde, E.I., Rajasekar, K.V.

Description: Crystal Structure of KorA-operator DNA complex (KorA-OA)
[[Category: Unreleased Structures]]
[[Category: Rajasekar, K.V]]
[[Category: White, S.A]]
[[Category: Hyde, E.I]]