5gux - Revision history

OCA at 11:43, 2 August 2023

OCA — Wed, 02 Aug 2023 11:43:19 GMT

←Older revision		Revision as of 11:43, 2 August 2023
Line 3:		Line 3:
	<StructureSection load='5gux' size='340' side='right'caption='[[5gux]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='5gux' size='340' side='right'caption='[[5gux]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gux]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [~~http~~://en.wikipedia.org/wiki/~~Pseudomonas_aeruginosa_pao1~~ Pseudomonas aeruginosa ~~pao1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GUX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gux]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GUX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=10M:DECYL+4-O-ALPHA-D-GLUCOPYRANOSYL-1-THIO-BETA-D-GLUCOPYRANOSIDE'>10M</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=XE:XENON'>XE</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]] 3.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o0r\|3o0r]], [[5guw\|5guw]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=10M:DECYL+4-O-ALPHA-D-GLUCOPYRANOSYL-1-THIO-BETA-D-GLUCOPYRANOSIDE'>10M</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=XE:XENON'>XE</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_(cytochrome_c) Nitric-oxide reductase (cytochrome c)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.5 1.7.2.5] </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=5gux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gux OCA], [https://pdbe.org/5gux PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gux RCSB], [https://www.ebi.ac.uk/pdbsum/5gux PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gux 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=5gux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gux OCA], [~~http~~://pdbe.org/5gux PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gux RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gux PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gux ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http://www.uniprot.org/uniprot/NORC_PSEAE NORC_PSEAE]] Component of the anaerobic respiratory chain that transforms nitrate to dinitrogen (denitrification). [[http~~://www.uniprot.org/uniprot/NORB_PSEAE NORB_PSEAE]] Component of the anaerobic respiratory chain that transforms nitrate to dinitrogen (denitrification). NorB is the catalytic subunit of the enzyme complex. Shows proton pump activity across the membrane in denitrifying bacterial cells. The mononitrogen reduction is probably coupled to electron transport phosphorylation (By similarity).	+	[https://www.uniprot.org/uniprot/NORB_PSEAE NORB_PSEAE] Component of the anaerobic respiratory chain that transforms nitrate to dinitrogen (denitrification). NorB is the catalytic subunit of the enzyme complex. Shows proton pump activity across the membrane in denitrifying bacterial cells. The mononitrogen reduction is probably coupled to electron transport phosphorylation (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 29:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Pseudomonas aeruginosa ~~pao1~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Ishii, S]]	+	[[Category: Ishii S]]
-	[[Category: Shiro, Y]]	+	[[Category: Shiro Y]]
-	[[Category: Sugimoto, H]]	+	[[Category: Sugimoto H]]
-	[[Category: Terasaka, E]]	+	[[Category: Terasaka E]]
-	[[Category: Tosha, T]]	+	[[Category: Tosha T]]
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Metal-binding~~]]	+

OCA at 06:43, 20 May 2020

OCA — Wed, 20 May 2020 06:43:53 GMT

←Older revision		Revision as of 06:43, 20 May 2020
Line 1:		Line 1:

	==Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon==		==Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon==
-	<StructureSection load='5gux' size='340' side='right' caption='[[5gux]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<StructureSection load='5gux' size='340' side='right'caption='[[5gux]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gux]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_pao1 Pseudomonas aeruginosa pao1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUX OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GUX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gux]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_pao1 Pseudomonas aeruginosa pao1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GUX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=10M:DECYL+4-O-ALPHA-D-GLUCOPYRANOSYL-1-THIO-BETA-D-GLUCOPYRANOSIDE'>10M</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=10M:DECYL+4-O-ALPHA-D-GLUCOPYRANOSYL-1-THIO-BETA-D-GLUCOPYRANOSIDE'>10M</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o0r\|3o0r]], [[5guw\|5guw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o0r\|3o0r]], [[5guw\|5guw]]</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_(cytochrome_c) Nitric-oxide reductase (cytochrome c)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.5 1.7.2.5] </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_(cytochrome_c) Nitric-oxide reductase (cytochrome c)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.5 1.7.2.5] </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=5gux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gux OCA], [http://pdbe.org/5gux PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gux RCSB], [http://www.ebi.ac.uk/pdbsum/5gux PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gux 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=5gux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gux OCA], [http://pdbe.org/5gux PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gux RCSB], [http://www.ebi.ac.uk/pdbsum/5gux PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gux ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5gux" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gux" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Pseudomonas aeruginosa pao1]]		[[Category: Pseudomonas aeruginosa pao1]]

OCA at 09:32, 27 September 2017

OCA — Wed, 27 Sep 2017 09:32:53 GMT

←Older revision		Revision as of 09:32, 27 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5gux is ~~ON HOLD until Paper~~ Publication	+	==Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon==
		+	<StructureSection load='5gux' size='340' side='right' caption='[[5gux]], [[Resolution\|resolution]] 3.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5gux]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_pao1 Pseudomonas aeruginosa pao1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GUX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=10M:DECYL+4-O-ALPHA-D-GLUCOPYRANOSYL-1-THIO-BETA-D-GLUCOPYRANOSIDE'>10M</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o0r\|3o0r]], [[5guw\|5guw]]</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_(cytochrome_c) Nitric-oxide reductase (cytochrome c)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.5 1.7.2.5] </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=5gux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gux OCA], [http://pdbe.org/5gux PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gux RCSB], [http://www.ebi.ac.uk/pdbsum/5gux PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gux ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NORC_PSEAE NORC_PSEAE]] Component of the anaerobic respiratory chain that transforms nitrate to dinitrogen (denitrification). [[http://www.uniprot.org/uniprot/NORB_PSEAE NORB_PSEAE]] Component of the anaerobic respiratory chain that transforms nitrate to dinitrogen (denitrification). NorB is the catalytic subunit of the enzyme complex. Shows proton pump activity across the membrane in denitrifying bacterial cells. The mononitrogen reduction is probably coupled to electron transport phosphorylation (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nitric oxide (NO) plays diverse and significant roles in biological processes despite its cytotoxicity, raising the question of how biological systems control the action of NO to minimize its cytotoxicity in cells. As a great example of such a system, we found a possibility that NO-generating nitrite reductase (NiR) forms a complex with NO-decomposing membrane-integrated NO reductase (NOR) to efficiently capture NO immediately after its production by NiR in anaerobic nitrate respiration called denitrification. The 3.2-A resolution structure of the complex of one NiR functional homodimer and two NOR molecules provides an idea of how these enzymes interact in cells, while the structure may not reflect the one in cells due to the membrane topology. Subsequent all-atom molecular dynamics (MD) simulations of the enzyme complex model in a membrane and structure-guided mutagenesis suggested that a few interenzyme salt bridges and coulombic interactions of NiR with the membrane could stabilize the complex of one NiR homodimer and one NOR molecule and contribute to rapid NO decomposition in cells. The MD trajectories of the NO diffusion in the NiR:NOR complex with the membrane showed that, as a plausible NO transfer mechanism, NO released from NiR rapidly migrates into the membrane, then binds to NOR. These results help us understand the mechanism of the cellular control of the action of cytotoxic NO.

-	~~Authors~~:	+	Dynamics of nitric oxide controlled by protein complex in bacterial system.,Terasaka E, Yamada K, Wang PH, Hosokawa K, Yamagiwa R, Matsumoto K, Ishii S, Mori T, Yagi K, Sawai H, Arai H, Sugimoto H, Sugita Y, Shiro Y, Tosha T Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):9888-9893. doi:, 10.1073/pnas.1621301114. Epub 2017 Aug 28. PMID:28847930<ref>PMID:28847930</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5gux" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Mus musculus]]
		+	[[Category: Pseudomonas aeruginosa pao1]]
		+	[[Category: Ishii, S]]
		+	[[Category: Shiro, Y]]
		+	[[Category: Sugimoto, H]]
		+	[[Category: Terasaka, E]]
		+	[[Category: Tosha, T]]
		+	[[Category: Membrane protein]]
		+	[[Category: Metal-binding]]

OCA at 10:30, 14 September 2016

OCA — Wed, 14 Sep 2016 10:30:35 GMT

←Older revision		Revision as of 10:30, 14 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Fri, 09 Sep 2016 12:06:57 GMT

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

←Older revision

Revision as of 12:06, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5gux is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Fri, 09 Sep 2016 12:06:56 GMT

New page: '''Unreleased structure''' The entry 5gux is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5gux is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]