5y5j - Revision history

OCA at 10:03, 6 September 2023

OCA — Wed, 06 Sep 2023 10:03:58 GMT

←Older revision		Revision as of 10:03, 6 September 2023
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	<StructureSection load='5y5j' size='340' side='right'caption='[[5y5j]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5y5j' size='340' side='right'caption='[[5y5j]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y5j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y5J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Y5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y5j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y5J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 2Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/Nitric_oxide_reductase_(NAD(P)(+)~~,~~_nitrous_oxide-forming) Nitric oxide reductase (NAD(P)(~~+~~), nitrous oxide-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.14 1.7.1.14]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=5y5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y5j OCA], [~~http~~://pdbe.org/5y5j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y5j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y5j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y5j 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=5y5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y5j OCA], [https://pdbe.org/5y5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y5j RCSB], [https://www.ebi.ac.uk/pdbsum/5y5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y5j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NOR_FUSOX NOR_FUSOX]] Nitric oxide reductase which is involved in a dissimilatory reduction of nitrite. Acts as a nitric oxide reductase. Is able to reduce nitrate and nitrite to a gaseous form of N(2)O when oxygen supply is limited or discontinued. May function as a detoxification mechanism.<ref>PMID:2040619</ref> <ref>PMID:12105197</ref>	+	[https://www.uniprot.org/uniprot/NOR_FUSOX NOR_FUSOX] Nitric oxide reductase which is involved in a dissimilatory reduction of nitrite. Acts as a nitric oxide reductase. Is able to reduce nitrate and nitrite to a gaseous form of N(2)O when oxygen supply is limited or discontinued. May function as a detoxification mechanism.<ref>PMID:2040619</ref> <ref>PMID:12105197</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Fusarium oxysporum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ago, H]]	+	[[Category: Ago H]]
-	[[Category: Hirata, K]]	+	[[Category: Hirata K]]
-	[[Category: Hisano, T]]	+	[[Category: Hisano T]]
-	[[Category: Ikemoto, Y]]	+	[[Category: Ikemoto Y]]
-	[[Category: Iwata, S]]	+	[[Category: Iwata S]]
-	[[Category: Kanematsu, Y]]	+	[[Category: Kanematsu Y]]
-	[[Category: Kimura, T]]	+	[[Category: Kimura T]]
-	[[Category: Kubo, M]]	+	[[Category: Kubo M]]
-	[[Category: Mizohata, E]]	+	[[Category: Mizohata E]]
-	[[Category: Murakami, H]]	+	[[Category: Murakami H]]
-	[[Category: Muramoto, K]]	+	[[Category: Muramoto K]]
-	[[Category: Nakane, T]]	+	[[Category: Nakane T]]
-	[[Category: Nango, E]]	+	[[Category: Nango E]]
-	[[Category: Nishida, T]]	+	[[Category: Nishida T]]
-	[[Category: Nomura, T]]	+	[[Category: Nomura T]]
-	[[Category: Nureki, O]]	+	[[Category: Nureki O]]
-	[[Category: Okubayashi, K]]	+	[[Category: Okubayashi K]]
-	[[Category: Owada, S]]	+	[[Category: Owada S]]
-	[[Category: Saeki, N]]	+	[[Category: Saeki N]]
-	[[Category: Sawai, H]]	+	[[Category: Sawai H]]
-	[[Category: Shiro, Y]]	+	[[Category: Shiro Y]]
-	[[Category: Sugahara, M]]	+	[[Category: Sugahara M]]
-	[[Category: Sugimoto, H]]	+	[[Category: Sugimoto H]]
-	[[Category: Takano, Y]]	+	[[Category: Takano Y]]
-	[[Category: Takeda, H]]	+	[[Category: Takeda H]]
-	[[Category: Tanaka, R]]	+	[[Category: Tanaka R]]
-	[[Category: Tono, K]]	+	[[Category: Tono K]]
-	[[Category: Tosha, T]]	+	[[Category: Tosha T]]
-	[[Category: Ueno, G]]	+	[[Category: Ueno G]]
-	[[Category: Yabashi, M]]	+	[[Category: Yabashi M]]
-	[[Category: Yamagiwa, R]]	+	[[Category: Yamagiwa R]]
-	[[Category: Yamamoto, M]]	+	[[Category: Yamamoto M]]
-	[[Category: Yamashita, A]]	+	[[Category: Yamashita A]]
-	[[Category: Yamashita, K]]	+	[[Category: Yamashita K]]
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:11, 21 October 2020

OCA — Wed, 21 Oct 2020 09:11:12 GMT

←Older revision		Revision as of 09:11, 21 October 2020
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	==Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state)==		==Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state)==
-	<StructureSection load='5y5j' size='340' side='right' caption='[[5y5j]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5y5j' size='340' side='right'caption='[[5y5j]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y5j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y5J OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y5j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y5J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Y5J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric_oxide_reductase_(NAD(P)(+),_nitrous_oxide-forming) Nitric oxide reductase (NAD(P)(+), nitrous oxide-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.14 1.7.1.14] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric_oxide_reductase_(NAD(P)(+),_nitrous_oxide-forming) Nitric oxide reductase (NAD(P)(+), nitrous oxide-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.14 1.7.1.14] </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=5y5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y5j OCA], [http://pdbe.org/5y5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y5j RCSB], [http://www.ebi.ac.uk/pdbsum/5y5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y5j ProSAT]</span></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=5y5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y5j OCA], [http://pdbe.org/5y5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y5j RCSB], [http://www.ebi.ac.uk/pdbsum/5y5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y5j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5y5j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5y5j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome P450 3D structures\|Cytochrome P450 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ago, H]]		[[Category: Ago, H]]
	[[Category: Hirata, K]]		[[Category: Hirata, K]]

OCA at 07:21, 6 December 2017

OCA — Wed, 06 Dec 2017 07:21:46 GMT

←Older revision		Revision as of 07:21, 6 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5y5j is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state)==
		+	<StructureSection load='5y5j' size='340' side='right' caption='[[5y5j]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5y5j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y5J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric_oxide_reductase_(NAD(P)(+),_nitrous_oxide-forming) Nitric oxide reductase (NAD(P)(+), nitrous oxide-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.14 1.7.1.14] </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=5y5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y5j OCA], [http://pdbe.org/5y5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y5j RCSB], [http://www.ebi.ac.uk/pdbsum/5y5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y5j ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NOR_FUSOX NOR_FUSOX]] Nitric oxide reductase which is involved in a dissimilatory reduction of nitrite. Acts as a nitric oxide reductase. Is able to reduce nitrate and nitrite to a gaseous form of N(2)O when oxygen supply is limited or discontinued. May function as a detoxification mechanism.<ref>PMID:2040619</ref> <ref>PMID:12105197</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Time-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers a crystallographic method to track enzymatic reactions. Here we demonstrate the application of this method using fungal NO reductase, a heme-containing enzyme, at room temperature. Twenty milliseconds after caged-NO photolysis, we identify a NO-bound form of the enzyme, which is an initial intermediate with a slightly bent Fe-N-O coordination geometry at a resolution of 2.1 A. The NO geometry is compatible with those analyzed by XFEL-based cryo-crystallography and QM/MM calculations, indicating that we obtain an intact Fe(3+)-NO coordination structure that is free of X-ray radiation damage. The slightly bent NO geometry is appropriate to prevent immediate NO dissociation and thus accept H(-) from NADH. The combination of using XFEL and a caged-compound is a powerful tool for determining functional enzyme structures during catalytic reactions at the atomic level.

-	~~Authors~~:	+	Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.,Tosha T, Nomura T, Nishida T, Saeki N, Okubayashi K, Yamagiwa R, Sugahara M, Nakane T, Yamashita K, Hirata K, Ueno G, Kimura T, Hisano T, Muramoto K, Sawai H, Takeda H, Mizohata E, Yamashita A, Kanematsu Y, Takano Y, Nango E, Tanaka R, Nureki O, Shoji O, Ikemoto Y, Murakami H, Owada S, Tono K, Yabashi M, Yamamoto M, Ago H, Iwata S, Sugimoto H, Shiro Y, Kubo M Nat Commun. 2017 Nov 17;8(1):1585. doi: 10.1038/s41467-017-01702-1. PMID:29147002<ref>PMID:29147002</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5y5j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ago, H]]
		+	[[Category: Hirata, K]]
		+	[[Category: Hisano, T]]
		+	[[Category: Ikemoto, Y]]
		+	[[Category: Iwata, S]]
		+	[[Category: Kanematsu, Y]]
		+	[[Category: Kimura, T]]
		+	[[Category: Kubo, M]]
		+	[[Category: Mizohata, E]]
		+	[[Category: Murakami, H]]
		+	[[Category: Muramoto, K]]
		+	[[Category: Nakane, T]]
		+	[[Category: Nango, E]]
		+	[[Category: Nishida, T]]
		+	[[Category: Nomura, T]]
		+	[[Category: Nureki, O]]
		+	[[Category: Okubayashi, K]]
		+	[[Category: Owada, S]]
		+	[[Category: Saeki, N]]
		+	[[Category: Sawai, H]]
		+	[[Category: Shiro, Y]]
		+	[[Category: Sugahara, M]]
		+	[[Category: Sugimoto, H]]
		+	[[Category: Takano, Y]]
		+	[[Category: Takeda, H]]
		+	[[Category: Tanaka, R]]
		+	[[Category: Tono, K]]
		+	[[Category: Tosha, T]]
		+	[[Category: Ueno, G]]
		+	[[Category: Yabashi, M]]
		+	[[Category: Yamagiwa, R]]
		+	[[Category: Yamamoto, M]]
		+	[[Category: Yamashita, A]]
		+	[[Category: Yamashita, K]]
		+	[[Category: Metal-binding]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "5y5j" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:09:59 GMT

Protected "5y5j" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:09, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y5j is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 16:09:58 GMT

New page: '''Unreleased structure''' The entry 5y5j is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5y5j is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]