5k0r - Revision history

OCA at 19:17, 20 September 2023

OCA — Wed, 20 Sep 2023 19:17:17 GMT

←Older revision		Revision as of 19:17, 20 September 2023
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	<StructureSection load='5k0r' size='340' side='right'caption='[[5k0r]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='5k0r' size='340' side='right'caption='[[5k0r]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k0r]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sheon Sheon~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K0R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K0R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k0r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis_MR-1 Shewanella oneidensis MR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K0R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8K6:OCTADECANE'>8K6</scene>, <scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</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]] 1.45Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4b5n\|4b5n]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8K6:OCTADECANE'>8K6</scene>, <scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sye4, SO_3392 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</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=5k0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k0r OCA], [https://pdbe.org/5k0r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k0r RCSB], [https://www.ebi.ac.uk/pdbsum/5k0r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k0r ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.30 1.5.1.30] </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=5k0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k0r OCA], [~~http~~://pdbe.org/5k0r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k0r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k0r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k0r ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8EBV3_SHEON Q8EBV3_SHEON]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Oxidoreductase]]~~	+	[[Category: Shewanella oneidensis MR-1]]
-	~~[[Category: Sheon~~]]	+	[[Category: Brige A]]
-	[[Category: Brige, A]]	+	[[Category: Elegheert J]]
-	[[Category: Elegheert, J]]	+	[[Category: Savvides SN]]
-	[[Category: Savvides~~, S N]]~~	+
-	~~[[Category: Cofactor-binding~~]]	+

OCA at 12:24, 17 July 2019

OCA — Wed, 17 Jul 2019 12:24:17 GMT

←Older revision		Revision as of 12:24, 17 July 2019
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	==Crystal structure of reduced Shewanella Yellow Enzyme 4 (SYE4)==		==Crystal structure of reduced Shewanella Yellow Enzyme 4 (SYE4)==
-	<StructureSection load='5k0r' size='340' side='right' caption='[[5k0r]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='5k0r' size='340' side='right'caption='[[5k0r]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5k0r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K0R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K0R FirstGlance]. <br>		<table><tr><td colspan='2'>[[5k0r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K0R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K0R FirstGlance]. <br>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Sheon]]		[[Category: Sheon]]

OCA at 10:17, 8 November 2017

OCA — Wed, 08 Nov 2017 10:17:11 GMT

←Older revision		Revision as of 10:17, 8 November 2017
Line 3:		Line 3:
	<StructureSection load='5k0r' size='340' side='right' caption='[[5k0r]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='5k0r' size='340' side='right' caption='[[5k0r]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k0r]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K0R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K0R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k0r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K0R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K0R FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8K6:OCTADECANE'>8K6</scene>, <scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8K6:OCTADECANE'>8K6</scene>, <scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4b5n\|4b5n]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4b5n\|4b5n]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sye4, SO_3392 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.30 1.5.1.30] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.30 1.5.1.30] </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=5k0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k0r OCA], [http://pdbe.org/5k0r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k0r RCSB], [http://www.ebi.ac.uk/pdbsum/5k0r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k0r ProSAT]</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=5k0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k0r OCA], [http://pdbe.org/5k0r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k0r RCSB], [http://www.ebi.ac.uk/pdbsum/5k0r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k0r ProSAT]</span></td></tr>
Line 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
		+	[[Category: Sheon]]
	[[Category: Brige, A]]		[[Category: Brige, A]]
	[[Category: Elegheert, J]]		[[Category: Elegheert, J]]
	[[Category: Savvides, S N]]		[[Category: Savvides, S N]]
	[[Category: Cofactor-binding]]		[[Category: Cofactor-binding]]

OCA at 10:27, 27 September 2017

OCA — Wed, 27 Sep 2017 10:27:26 GMT

←Older revision		Revision as of 10:27, 27 September 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5k0r is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of reduced Shewanella Yellow Enzyme 4 (SYE4)==
		+	<StructureSection load='5k0r' size='340' side='right' caption='[[5k0r]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k0r]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K0R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K0R FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8K6:OCTADECANE'>8K6</scene>, <scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4b5n\|4b5n]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.30 1.5.1.30] </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=5k0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k0r OCA], [http://pdbe.org/5k0r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k0r RCSB], [http://www.ebi.ac.uk/pdbsum/5k0r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k0r ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Shewanella oneidensis, a Gram-negative gamma-proteobacterium with an extensive redox capacity, possesses four old yellow enzyme (OYE) homologs. Of these, Shewanella yellow enzyme 4 (SYE4) is implicated in resistance to oxidative stress. Here, we present a series of high-resolution crystal structures for SYE4 in the oxidized and reduced states, and in complex with phenolic ligands and the nitro-aromatic explosive picric acid. The structures unmask new features, including the identification of a binding platform for long-chain hydrophobic molecules. Furthermore, we present the first structural observation of a hydride-Meisenheimer complex of picric acid with a flavoenzyme. Overall, our study exposes the binding promiscuity of SYE4 toward a variety of electrophilic substrates and is consistent with a general detoxification function for SYE4.

-	~~Authors~~:	+	Structural dissection of Shewanella oneidensis old yellow enzyme 4 bound to a Meisenheimer complex and (nitro)phenolic ligands.,Elegheert J, Brige A, Van Beeumen J, Savvides SN FEBS Lett. 2017 Sep 4. doi: 10.1002/1873-3468.12833. PMID:28869767<ref>PMID:28869767</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5k0r" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Oxidoreductase]]
		+	[[Category: Brige, A]]
		+	[[Category: Elegheert, J]]
		+	[[Category: Savvides, S N]]
		+	[[Category: Cofactor-binding]]

OCA: Protected "5k0r" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:09:26 GMT

Protected "5k0r" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:09, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k0r is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Jun 2016 14:09:24 GMT

New page: '''Unreleased structure''' The entry 5k0r is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5k0r is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]