3jv9 - Revision history

OCA at 09:43, 26 December 2018

OCA — Wed, 26 Dec 2018 09:43:54 GMT

←Older revision		Revision as of 09:43, 26 December 2018
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jv/3jv9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jv/3jv9_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>

OCA at 16:45, 5 August 2016

OCA — Fri, 05 Aug 2016 16:45:43 GMT

←Older revision		Revision as of 16:45, 5 August 2016
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		+
	==The structure of a reduced form of OxyR from N. meningitidis==		==The structure of a reduced form of OxyR from N. meningitidis==
	<StructureSection load='3jv9' size='340' side='right' caption='[[3jv9]], [[Resolution\|resolution]] 2.39Å' scene=''>		<StructureSection load='3jv9' size='340' side='right' caption='[[3jv9]], [[Resolution\|resolution]] 2.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jv9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Neisseria_meningitidis Neisseria meningitidis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JV9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JV9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jv9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neimb Neimb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JV9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JV9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NMB0173 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~487 Neisseria meningitidis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NMB0173 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=122586 NEIMB])</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=3jv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jv9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jv9 RCSB], [http://www.ebi.ac.uk/pdbsum/3jv9 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=3jv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jv9 OCA], [http://pdbe.org/3jv9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jv9 RCSB], [http://www.ebi.ac.uk/pdbsum/3jv9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jv9 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<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=3jv9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3jv9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Neisseria meningitidis~~]]	+	[[Category: Neimb]]
	[[Category: OPPF, Oxford Protein Production Facility]]		[[Category: OPPF, Oxford Protein Production Facility]]
	[[Category: Owens, R J]]		[[Category: Owens, R J]]

OCA at 17:17, 18 December 2014

OCA — Thu, 18 Dec 2014 17:17:22 GMT

←Older revision		Revision as of 17:17, 18 December 2014
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-	~~{{STRUCTURE_3jv9~~\| ~~PDB~~=3jv9 \| ~~SCENE~~= }}	+	==The structure of a reduced form of OxyR from N. meningitidis==
-	===~~The~~ structure of a reduced form of OxyR from N. meningitidis~~===~~	+	<StructureSection load='3jv9' size='340' side='right' caption='[[3jv9]], [[Resolution\|resolution]] 2.39Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20478059}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3jv9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neisseria_meningitidis Neisseria meningitidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JV9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JV9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NMB0173 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=487 Neisseria meningitidis])</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=3jv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jv9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jv9 RCSB], [http://www.ebi.ac.uk/pdbsum/3jv9 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/jv/3jv9_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 ==
		+	BACKGROUND: Survival of the human pathogen, Neisseria meningitidis, requires an effective response to oxidative stress resulting from the release of hydrogen peroxide by cells of the human immune system. In N. meningitidis, expression of catalase, which is responsible for detoxifying hydrogen peroxide, is controlled by OxyR, a redox responsive LysR-type regulator. OxyR responds directly to intracellular hydrogen peroxide through the reversible formation of a disulphide bond between C199 and C208 in the regulatory domain of the protein. RESULTS: We report the first crystal structure of the regulatory domain of an OxyR protein (NMB0173 from N. meningitidis) in the reduced state i.e. with cysteines at positions 199 and 208. The protein was crystallized under reducing conditions and the structure determined to a resolution of 2.4 A. The overall fold of the Neisseria OxyR shows a high degree of similarity to the structure of a C199S mutant OxyR from E. coli, which cannot form the redox sensitive disulphide. In the neisserial structure, C199 is located at the start of helix alpha3, separated by 18 A from C208, which is positioned between helices alpha3 and alpha4. In common with other LysR-type regulators, full length OxyR proteins are known to assemble into tetramers. Modelling of the full length neisserial OxyR as a tetramer indicated that C199 and C208 are located close to the dimer-dimer interface in the assembled tetramer. The formation of the C199-C208 disulphide may thus affect the quaternary structure of the protein. CONCLUSION: Given the high level of structural similarity between OxyR from N. meningitidis and E. coli, we conclude that the redox response mechanism is likely to be similar in both species, involving the reversible formation of a disulphide between C199-C208. Modelling suggests that disulphide formation would directly affect the interface between regulatory domains in an OxyR tetramer which in turn may lead to an alteration in the spacing/orientation of the DNA-binding domains and hence the interaction of OxyR with its DNA binding sites.

-	~~==About this Structure==~~	+	The structure of a reduced form of OxyR from Neisseria meningitidis.,Sainsbury S, Ren J, Nettleship JE, Saunders NJ, Stuart DI, Owens RJ BMC Struct Biol. 2010 May 17;10:10. PMID:20478059<ref>PMID:20478059</ref>
-	~~[[3jv9]] is~~ a ~~2 chain structure with sequence~~ from ~~[http://en.wikipedia.org/wiki/Neisseria_meningitidis~~ Neisseria meningitidis]. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann.ac.il~~/~~oca-bin/ocashort?id=3JV9 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:020478059</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Neisseria meningitidis]]		[[Category: Neisseria meningitidis]]
-	[[Category: OPPF, Oxford Protein Production Facility.]]	+	[[Category: OPPF, Oxford Protein Production Facility]]
-	[[Category: Owens, R J.]]	+	[[Category: Owens, R J]]
-	[[Category: Ren, J.]]	+	[[Category: Ren, J]]
-	[[Category: Sainsbury, S.]]	+	[[Category: Sainsbury, S]]
-	[[Category: Stuart, D I.]]	+	[[Category: Stuart, D I]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
	[[Category: Lttr]]		[[Category: Lttr]]

OCA: Protected "3jv9" [edit=sysop:move=sysop]

OCA — Wed, 27 Mar 2013 09:40:03 GMT

Protected "3jv9" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:40, 27 March 2013

OCA at 09:39, 27 March 2013

OCA — Wed, 27 Mar 2013 09:39:59 GMT

←Older revision		Revision as of 09:39, 27 March 2013
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-	{{Seed}}
-	[[Image:3jv9.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3jv9", 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_3jv9\| PDB=3jv9 \| SCENE= }}		{{STRUCTURE_3jv9\| PDB=3jv9 \| SCENE= }}
-
	===The structure of a reduced form of OxyR from N. meningitidis===		===The structure of a reduced form of OxyR from N. meningitidis===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20478059}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20478059 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20478059}}		{{ABSTRACT_PUBMED_20478059}}

	==About this Structure==		==About this Structure==
-	~~3JV9~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Neisseria_meningitidis Neisseria meningitidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JV9 OCA].	+	[[3jv9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neisseria_meningitidis Neisseria meningitidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JV9 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20478059~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020478059</ref><references group="xtra"/><references/>
	[[Category: Neisseria meningitidis]]		[[Category: Neisseria meningitidis]]
	[[Category: OPPF, Oxford Protein Production Facility.]]		[[Category: OPPF, Oxford Protein Production Facility.]]
Line 40:		Line 24:
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:38:17 2010''

OCA at 04:33, 16 June 2010

OCA — Wed, 16 Jun 2010 04:33:17 GMT

←Older revision		Revision as of 04:33, 16 June 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3jv9.jpg\|left\|200px]]

-	The ~~entry 3jv9~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3jv9", 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_3jv9\| PDB=3jv9 \| SCENE= }}

-	~~Authors: Sainsbury, S~~.~~, Ren, J., Stuart, D.I., Owens, R.J., Oxford Protein Production Facility (OPPF)~~	+	===The structure of a reduced form of OxyR from N. meningitidis===

-	Description: The structure of a reduced form of OxyR from N. meningitidis

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Oct 14 10~~:06:~~19 2009~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20478059}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20478059 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20478059}}
		+
		+	==About this Structure==
		+	3JV9 is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Neisseria_meningitidis Neisseria meningitidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JV9 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20478059</ref><references group="xtra"/>
		+	[[Category: Neisseria meningitidis]]
		+	[[Category: OPPF, Oxford Protein Production Facility.]]
		+	[[Category: Owens, R J.]]
		+	[[Category: Ren, J.]]
		+	[[Category: Sainsbury, S.]]
		+	[[Category: Stuart, D I.]]
		+	[[Category: Dna-binding]]
		+	[[Category: Lttr]]
		+	[[Category: Lysr-type transcriptional regulator]]
		+	[[Category: Oppf]]
		+	[[Category: Oppf3291]]
		+	[[Category: Oxford protein production facility]]
		+	[[Category: Redox]]
		+	[[Category: Structural genomic]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:38:17 2010''

OCA at 08:06, 14 October 2009

OCA — Wed, 14 Oct 2009 08:06:19 GMT

←Older revision		Revision as of 08:06, 14 October 2009
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3jv9 is ON HOLD	+	The entry 3jv9 is ON HOLD until Paper Publication

	Authors: Sainsbury, S., Ren, J., Stuart, D.I., Owens, R.J., Oxford Protein Production Facility (OPPF)		Authors: Sainsbury, S., Ren, J., Stuart, D.I., Owens, R.J., Oxford Protein Production Facility (OPPF)
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	Description: The structure of a reduced form of OxyR from N. meningitidis		Description: The structure of a reduced form of OxyR from N. meningitidis

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Sep 30 09~~:00:09 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 14 10:06:19 2009''

OCA at 07:00, 30 September 2009

OCA — Wed, 30 Sep 2009 07:00:09 GMT

←Older revision		Revision as of 07:00, 30 September 2009
Line 3:		Line 3:
	The entry 3jv9 is ON HOLD		The entry 3jv9 is ON HOLD

-	Authors: Sainsbury, S. , Ren, J. , ~~STUART~~, D.I., Owens, R.J. , Oxford Protein Production Facility (OPPF)	+	Authors: Sainsbury, S., Ren, J., Stuart, D.I., Owens, R.J., Oxford Protein Production Facility (OPPF)

	Description: The structure of a reduced form of OxyR from N. meningitidis		Description: The structure of a reduced form of OxyR from N. meningitidis

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep ~~23 08~~:31:17 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 30 09:00:09 2009''

OCA: New page: '''Unreleased structure''' The entry 3jv9 is ON HOLD Authors: Sainsbury, S. , Ren, J. , STUART, D.I., Owens, R.J. , Oxford Protein Production Facility (OPPF) Description: The structure...

OCA — Wed, 23 Sep 2009 05:31:18 GMT

New page: '''Unreleased structure''' The entry 3jv9 is ON HOLD Authors: Sainsbury, S. , Ren, J. , STUART, D.I., Owens, R.J. , Oxford Protein Production Facility (OPPF) Description: The structure...

New page

'''Unreleased structure'''

The entry 3jv9 is ON HOLD

Authors: Sainsbury, S. , Ren, J. , STUART, D.I., Owens, R.J. , Oxford Protein Production Facility (OPPF)

Description: The structure of a reduced form of OxyR from N. meningitidis

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 23 08:31:17 2009''