3vca - Revision history

OCA at 18:38, 27 July 2022

2022-07-27T18:38:01Z

←Older revision		Revision as of 18:38, 27 July 2022
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	==Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman and UV-visible Spectroscopic Analysis of a Rieske-type Demethylase==		==Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman and UV-visible Spectroscopic Analysis of a Rieske-type Demethylase==
-	<StructureSection load='3vca' size='340' side='right' caption='[[3vca]], [[Resolution\|resolution]] 1.59Å' scene=''>	+	<StructureSection load='3vca' size='340' side='right'caption='[[3vca]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vca]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ensifer_meliloti Ensifer meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VCA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VCA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vca]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ensifer_meliloti Ensifer meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VCA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vcp\|3vcp]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vcp\|3vcp]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NP_435646, RA0400, SMa0751 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266834 Ensifer meliloti])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NP_435646, RA0400, SMa0751 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266834 Ensifer meliloti])</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=3vca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vca OCA], [~~http~~://pdbe.org/3vca PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vca RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vca PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vca 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=3vca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vca OCA], [https://pdbe.org/3vca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vca RCSB], [https://www.ebi.ac.uk/pdbsum/3vca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vca ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Ensifer meliloti]]		[[Category: Ensifer meliloti]]
		+	[[Category: Large Structures]]
	[[Category: Allen, K N]]		[[Category: Allen, K N]]
	[[Category: Cho, E]]		[[Category: Cho, E]]

OCA at 12:55, 11 August 2016

2016-08-11T12:55:39Z

←Older revision		Revision as of 12:55, 11 August 2016
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		+
	==Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman and UV-visible Spectroscopic Analysis of a Rieske-type Demethylase==		==Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman and UV-visible Spectroscopic Analysis of a Rieske-type Demethylase==
	<StructureSection load='3vca' size='340' side='right' caption='[[3vca]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='3vca' size='340' side='right' caption='[[3vca]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vca]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sinorhizobium_meliloti Sinorhizobium~~ meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VCA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VCA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vca]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ensifer_meliloti Ensifer meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VCA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VCA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vcp\|3vcp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vcp\|3vcp]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NP_435646, RA0400, SMa0751 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~382 Sinorhizobium~~ meliloti])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NP_435646, RA0400, SMa0751 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266834 Ensifer meliloti])</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=3vca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vca OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vca RCSB], [http://www.ebi.ac.uk/pdbsum/3vca 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=3vca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vca OCA], [http://pdbe.org/3vca PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vca RCSB], [http://www.ebi.ac.uk/pdbsum/3vca PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vca ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 3vca" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sinorhizobium~~ meliloti]]	+	[[Category: Ensifer meliloti]]
	[[Category: Allen, K N]]		[[Category: Allen, K N]]
	[[Category: Cho, E]]		[[Category: Cho, E]]

OCA at 09:48, 4 January 2015

2015-01-04T09:48:52Z

←Older revision		Revision as of 09:48, 4 January 2015
Line 1:		Line 1:
-	[[~~Image:~~3vca.~~png~~\|~~left~~\|~~200px~~]]	+	==Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman and UV-visible Spectroscopic Analysis of a Rieske-type Demethylase==
		+	<StructureSection load='3vca' size='340' side='right' caption='[[3vca]], [[Resolution\|resolution]] 1.59Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3vca]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VCA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VCA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vcp\|3vcp]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NP_435646, RA0400, SMa0751 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 Sinorhizobium meliloti])</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=3vca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vca OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vca RCSB], [http://www.ebi.ac.uk/pdbsum/3vca PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Herein, the structure resulting from in situ turnover in a chemically challenging quaternary ammonium oxidative demethylation reaction was captured via crystallographic analysis and analyzed via single-crystal spectroscopy. Crystal structures were determined for the Rieske-type monooxygenase, stachydrine demethylase, in the unliganded state (at 1.6 A resolution) and in the product complex (at 2.2 A resolution). The ligand complex was obtained from enzyme aerobically cocrystallized with the substrate stachydrine (N,N-dimethylproline). The ligand electron density in the complex was interpreted as proline, generated within the active site at 100 K by the absorption of X-ray photon energy and two consecutive demethylation cycles. The oxidation state of the Rieske iron-sulfur cluster was characterized by UV-visible spectroscopy throughout X-ray data collection in conjunction with resonance Raman spectra collected before and after diffraction data. Shifts in the absorption band wavelength and intensity as a function of absorbed X-ray dose demonstrated that the Rieske center was reduced by solvated electrons generated by X-ray photons; the kinetics of the reduction process differed dramatically for the liganded complex compared to unliganded demethylase, which may correspond to the observed turnover in the crystal.

-	<!--	+	Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman, and UV-Visible Spectroscopic Analysis of a Rieske-Type Demethylase.,Daughtry KD, Xiao Y, Stoner-Ma D, Cho E, Orville AM, Liu P, Allen KN J Am Chem Soc. 2012 Jan 26. PMID:22224443<ref>PMID:22224443</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3vca"~~, ~~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_3vca\| PDB=3vca \| SCENE= }}~~	+

-	~~===Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic~~, ~~Resonance Raman and UV-visible Spectroscopic Analysis~~ of ~~a Rieske-type Demethylase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22224443}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22224443 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22224443}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3vca]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VCA OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022224443<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]
-	[[Category: Allen, K N.]]	+	[[Category: Allen, K N]]
-	[[Category: Cho, E.]]	+	[[Category: Cho, E]]
-	[[Category: Daughtry, K D.]]	+	[[Category: Daughtry, K D]]
-	[[Category: Liu, P.]]	+	[[Category: Liu, P]]
-	[[Category: Orville, A M.]]	+	[[Category: Orville, A M]]
-	[[Category: Stoner-Ma, D.]]	+	[[Category: Stoner-Ma, D]]
-	[[Category: Xiao, Y.]]	+	[[Category: Xiao, Y]]
	[[Category: Mononuclear non-heme iron]]		[[Category: Mononuclear non-heme iron]]
	[[Category: N-demethylase]]		[[Category: N-demethylase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rieske-type]]		[[Category: Rieske-type]]

OCA at 06:39, 22 February 2012

2012-02-22T06:39:26Z

←Older revision		Revision as of 06:39, 22 February 2012
Line 1:		Line 1:
-	[[Image:3vca.~~jpg~~\|left\|200px]]	+	[[Image:3vca.png\|left\|200px]]

	<!--		<!--

OCA at 06:29, 8 February 2012

2012-02-08T06:29:25Z

←Older revision		Revision as of 06:29, 8 February 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3vca.jpg\|left\|200px]]

-	The ~~entry 3vca~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3vca", 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_3vca\| PDB=3vca \| SCENE= }}

-	~~Authors~~: ~~Daughtry~~, ~~K.D., Xiao, Y., Stoner~~-~~Ma, D., Cho, E., Orville, A.M., Liu, P., Allen, K.N.~~	+	===Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman and UV-visible Spectroscopic Analysis of a Rieske-type Demethylase===

-	~~Description~~: ~~Quaternary Ammonium Oxidative Demethylation~~: X-~~ray Crystallographic~~, ~~Resonance Raman and UV~~-~~visible Spectroscopic Analysis of a~~ Rieske-type ~~Demethylase~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22224443}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22224443 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22224443}}
		+
		+	==About this Structure==
		+	[[3vca]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VCA OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022224443</ref><references group="xtra"/>
		+	[[Category: Sinorhizobium meliloti]]
		+	[[Category: Allen, K N.]]
		+	[[Category: Cho, E.]]
		+	[[Category: Daughtry, K D.]]
		+	[[Category: Liu, P.]]
		+	[[Category: Orville, A M.]]
		+	[[Category: Stoner-Ma, D.]]
		+	[[Category: Xiao, Y.]]
		+	[[Category: Mononuclear non-heme iron]]
		+	[[Category: N-demethylase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rieske-type]]

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

2012-01-11T06:01:11Z

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

←Older revision

Revision as of 06:01, 11 January 2012

OCA: New page: '''Unreleased structure''' The entry 3vca is ON HOLD Authors: Daughtry, K.D., Xiao, Y., Stoner-Ma, D., Cho, E., Orville, A.M., Liu, P., Allen, K.N. Description: Quaternary Ammonium Oxi...

2012-01-11T06:01:10Z

New page: '''Unreleased structure''' The entry 3vca is ON HOLD Authors: Daughtry, K.D., Xiao, Y., Stoner-Ma, D., Cho, E., Orville, A.M., Liu, P., Allen, K.N. Description: Quaternary Ammonium Oxi...

New page

'''Unreleased structure'''

The entry 3vca is ON HOLD

Authors: Daughtry, K.D., Xiao, Y., Stoner-Ma, D., Cho, E., Orville, A.M., Liu, P., Allen, K.N.

Description: Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman and UV-visible Spectroscopic Analysis of a Rieske-type Demethylase