5hbl - Revision history

OCA at 07:29, 9 August 2023

OCA — Wed, 09 Aug 2023 07:29:48 GMT

←Older revision		Revision as of 07:29, 9 August 2023
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	<StructureSection load='5hbl' size='340' side='right'caption='[[5hbl]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='5hbl' size='340' side='right'caption='[[5hbl]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hbl]] is a 1 chain structure with sequence from [https://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=5HBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HBL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hbl]] is a 1 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=5HBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HBL FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=SNC:S~~-~~NITROSO-CYSTEINE'>SNC</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]] 1.617Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ygaP, b2668, JW2643 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene></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=5hbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hbl OCA], [https://pdbe.org/5hbl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hbl RCSB], [https://www.ebi.ac.uk/pdbsum/5hbl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hbl 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=5hbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hbl OCA], [https://pdbe.org/5hbl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hbl RCSB], [https://www.ebi.ac.uk/pdbsum/5hbl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hbl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/YGAP_ECOLI YGAP_ECOLI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Choe, S]]	+	[[Category: Choe S]]
-	[[Category: Eichmann, C]]	+	[[Category: Eichmann C]]
-	[[Category: Kwiatkowski, W]]	+	[[Category: Kwiatkowski W]]
-	[[Category: Lipton~~, S A~~]]	+	[[Category: Lipton SA]]
-	[[Category: Maslennikov, I]]	+	[[Category: Maslennikov I]]
-	[[Category: Nakamura, T]]	+	[[Category: Nakamura T]]
-	[[Category: Riek, R]]	+	[[Category: Riek R]]
-	[[Category: Tzitzilonis, C]]	+	[[Category: Tzitzilonis C]]
-	~~[[Category: S-nitrosylation]]~~	+
-	~~[[Category: S-sulfhydration. rhodanese]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:01, 8 September 2021

OCA — Wed, 08 Sep 2021 09:01:35 GMT

←Older revision		Revision as of 09:01, 8 September 2021
Line 3:		Line 3:
	<StructureSection load='5hbl' size='340' side='right'caption='[[5hbl]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='5hbl' size='340' side='right'caption='[[5hbl]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hbl]] is a 1 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=5HBL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HBL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hbl]] is a 1 chain structure with sequence from [https://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=5HBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HBL FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ygaP, b2668, JW2643 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ygaP, b2668, JW2643 ([https://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~~://proteopedia.org/fgij/fg.htm?mol=5hbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hbl OCA], [~~http~~://pdbe.org/5hbl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hbl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hbl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hbl 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=5hbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hbl OCA], [https://pdbe.org/5hbl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hbl RCSB], [https://www.ebi.ac.uk/pdbsum/5hbl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hbl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:58, 20 May 2020

OCA — Wed, 20 May 2020 06:58:28 GMT

←Older revision		Revision as of 06:58, 20 May 2020
Line 1:		Line 1:

	==Native rhodanese domain of YgaP prepared with 1mM DDT is S-nitrosylated==		==Native rhodanese domain of YgaP prepared with 1mM DDT is S-nitrosylated==
-	<StructureSection load='5hbl' size='340' side='right' caption='[[5hbl]], [[Resolution\|resolution]] 1.62Å' scene=''>	+	<StructureSection load='5hbl' size='340' side='right'caption='[[5hbl]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hbl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HBL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HBL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hbl]] is a 1 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=5HBL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HBL FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene></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=5hbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hbl OCA], [http://pdbe.org/5hbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hbl RCSB], [http://www.ebi.ac.uk/pdbsum/5hbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hbl ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ygaP, b2668, JW2643 ([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://proteopedia.org/fgij/fg.htm?mol=5hbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hbl OCA], [http://pdbe.org/5hbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hbl RCSB], [http://www.ebi.ac.uk/pdbsum/5hbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hbl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Choe, S]]		[[Category: Choe, S]]
	[[Category: Eichmann, C]]		[[Category: Eichmann, C]]

OCA at 16:04, 10 August 2016

OCA — Wed, 10 Aug 2016 16:04:30 GMT

←Older revision		Revision as of 16:04, 10 August 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5hbl is ~~ON HOLD until Paper~~ Publication	+	==Native rhodanese domain of YgaP prepared with 1mM DDT is S-nitrosylated==
		+	<StructureSection load='5hbl' size='340' side='right' caption='[[5hbl]], [[Resolution\|resolution]] 1.62Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hbl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HBL FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SNC:S-NITROSO-CYSTEINE'>SNC</scene></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=5hbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hbl OCA], [http://pdbe.org/5hbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hbl RCSB], [http://www.ebi.ac.uk/pdbsum/5hbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hbl ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	S-Nitrosylation is well established as an important post-translational regulator in protein function and signaling. However, relatively little is known about its structural and dynamical consequences. We have investigated the effects of S-nitrosylation on the rhodanese domain of the Escherichia coli integral membrane protein YgaP by NMR, X-ray crystallography, and mass spectrometry. The results show that the active cysteine in the rhodanese domain of YgaP is subjected to two competing modifications: S-nitrosylation and S-sulfhydration, which are naturally occurring in vivo. It has been observed that in addition to inhibition of the sulfur transfer activity, S-nitrosylation of the active site residue Cys63 causes an increase in slow motion and a displacement of helix 5 due to a weakening of the interaction between the active site and the helix dipole. These findings provide an example of how nitrosative stress can exert action at the atomic level.

-	~~Authors: Eichmann~~, C., Tzitzilonis, C., Nakamura, T., Kwiatkowski, W., Maslennikov, I., Choe, S., Lipton, S.A., ~~Riek, R~~.	+	S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein.,Eichmann C, Tzitzilonis C, Nakamura T, Kwiatkowski W, Maslennikov I, Choe S, Lipton SA, Riek R J Mol Biol. 2016 Jul 27. pii: S0022-2836(16)30255-8. doi:, 10.1016/j.jmb.2016.07.010. PMID:27473602<ref>PMID:27473602</ref>

-	~~Description: Native rhodanese domain~~ of ~~YgaP prepared with 1mM DDT is~~ S~~-nitrosylated~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5hbl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Choe, S]]		[[Category: Choe, S]]
-	[[Category: Tzitzilonis, C]]
-	[[Category: Kwiatkowski, W]]
-	[[Category: Riek, R]]
-	[[Category: Lipton, S.A]]
	[[Category: Eichmann, C]]		[[Category: Eichmann, C]]
		+	[[Category: Kwiatkowski, W]]
		+	[[Category: Lipton, S A]]
	[[Category: Maslennikov, I]]		[[Category: Maslennikov, I]]
	[[Category: Nakamura, T]]		[[Category: Nakamura, T]]
		+	[[Category: Riek, R]]
		+	[[Category: Tzitzilonis, C]]
		+	[[Category: S-nitrosylation]]
		+	[[Category: S-sulfhydration. rhodanese]]
		+	[[Category: Transferase]]

OCA at 15:13, 20 January 2016

OCA — Wed, 20 Jan 2016 15:13:04 GMT

←Older revision		Revision as of 15:13, 20 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hbl is ON HOLD	+	The entry 5hbl is ON HOLD until Paper Publication

-	Authors: ~~Cedric~~ Eichmann, ~~Christos~~ Tzitzilonis, ~~Tomohiro~~ Nakamura, ~~Witek~~ Kwiatkowski, ~~Innokentiy~~ Maslennikov, ~~Senyon~~ Choe, ~~Stuart A~~. Lipton, ~~Roland~~ Riek	+	Authors: Eichmann, C., Tzitzilonis, C., Nakamura, T., Kwiatkowski, W., Maslennikov, I., Choe, S., Lipton, S.A., Riek, R.

	Description: Native rhodanese domain of YgaP prepared with 1mM DDT is S-nitrosylated		Description: Native rhodanese domain of YgaP prepared with 1mM DDT is S-nitrosylated
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Cedric Eichmann~~, ~~Christos~~ Tzitzilonis, ~~Tomohiro Nakamura, Witek~~ Kwiatkowski, ~~Innokentiy Maslennikov~~, ~~Senyon Choe~~, ~~Stuart A~~. ~~Lipton~~, ~~Roland Riek~~]]	+	[[Category: Choe, S]]
		+	[[Category: Tzitzilonis, C]]
		+	[[Category: Kwiatkowski, W]]
		+	[[Category: Riek, R]]
		+	[[Category: Lipton, S.A]]
		+	[[Category: Eichmann, C]]
		+	[[Category: Maslennikov, I]]
		+	[[Category: Nakamura, T]]

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

OCA — Wed, 13 Jan 2016 18:46:06 GMT

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

←Older revision

Revision as of 18:46, 13 January 2016

OCA: New page: '''Unreleased structure''' The entry 5hbl is ON HOLD Authors: Cedric Eichmann, Christos Tzitzilonis, Tomohiro Nakamura, Witek Kwiatkowski, Innokentiy Maslennikov, Senyon Choe, Stuart A....

OCA — Wed, 13 Jan 2016 18:46:05 GMT

New page: '''Unreleased structure''' The entry 5hbl is ON HOLD Authors: Cedric Eichmann, Christos Tzitzilonis, Tomohiro Nakamura, Witek Kwiatkowski, Innokentiy Maslennikov, Senyon Choe, Stuart A....

New page

'''Unreleased structure'''

The entry 5hbl is ON HOLD

Authors: Cedric Eichmann, Christos Tzitzilonis, Tomohiro Nakamura, Witek Kwiatkowski, Innokentiy Maslennikov, Senyon Choe, Stuart A. Lipton, Roland Riek

Description: Native rhodanese domain of YgaP prepared with 1mM DDT is S-nitrosylated
[[Category: Unreleased Structures]]
[[Category: Cedric Eichmann, Christos Tzitzilonis, Tomohiro Nakamura, Witek Kwiatkowski, Innokentiy Maslennikov, Senyon Choe, Stuart A. Lipton, Roland Riek]]