4xyd - Revision history

OCA at 10:51, 10 January 2024

2024-01-10T10:51:22Z

←Older revision		Revision as of 10:51, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xyd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Roseobacter_denitrificans_OCh_114 Roseobacter denitrificans OCh 114]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XYD FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xyd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Roseobacter_denitrificans_OCh_114 Roseobacter denitrificans OCh 114]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XYD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=UNL:UNKNOWN+LIGAND'>UNL</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]] 2.85Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=UNL:UNKNOWN+LIGAND'>UNL</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=4xyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyd OCA], [https://pdbe.org/4xyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xyd RCSB], [https://www.ebi.ac.uk/pdbsum/4xyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xyd 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=4xyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyd OCA], [https://pdbe.org/4xyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xyd RCSB], [https://www.ebi.ac.uk/pdbsum/4xyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xyd ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:58, 26 April 2023

2023-04-26T17:58:23Z

←Older revision		Revision as of 17:58, 26 April 2023
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	<StructureSection load='4xyd' size='340' side='right'caption='[[4xyd]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='4xyd' size='340' side='right'caption='[[4xyd]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xyd]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Erythrobacter_sp._(strain_och_114) Erythrobacter sp. (strain och~~ 114)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XYD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xyd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Roseobacter_denitrificans_OCh_114 Roseobacter denitrificans OCh 114]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XYD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=UNL:UNKNOWN+LIGAND'>UNL</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=UNL:UNKNOWN+LIGAND'>UNL</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=4xyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyd OCA], [https://pdbe.org/4xyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xyd RCSB], [https://www.ebi.ac.uk/pdbsum/4xyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xyd 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=4xyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyd OCA], [~~http~~://pdbe.org/4xyd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xyd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xyd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xyd ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q16A04_ROSDO Q16A04_ROSDO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Crow, A~~]]	+	[[Category: Roseobacter denitrificans OCh 114]]
-	[[Category: ~~Heme copper oxidase superfamily]]~~	+	[[Category: Crow A]]
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Nitric oxide reductase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 23:29, 5 June 2019

2019-06-05T23:29:44Z

←Older revision		Revision as of 23:29, 5 June 2019
Line 1:		Line 1:

	==Nitric oxide reductase from Roseobacter denitrificans (RdNOR)==		==Nitric oxide reductase from Roseobacter denitrificans (RdNOR)==
-	<StructureSection load='4xyd' size='340' side='right' caption='[[4xyd]], [[Resolution\|resolution]] 2.85Å' scene=''>	+	<StructureSection load='4xyd' size='340' side='right'caption='[[4xyd]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xyd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Roseobacter_denitrificans_~~(~~strain_atcc_33942_/_och_114~~) ~~Roseobacter denitrificans~~ (strain ~~atcc 33942 /~~ och 114)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XYD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xyd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Erythrobacter_sp._(strain_och_114) Erythrobacter sp. (strain och 114)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XYD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=UNL:UNKNOWN+LIGAND'>UNL</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='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>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Crow, A]]		[[Category: Crow, A]]
	[[Category: Heme copper oxidase superfamily]]		[[Category: Heme copper oxidase superfamily]]

OCA at 02:32, 13 July 2016

2016-07-13T02:32:42Z

←Older revision		Revision as of 02:32, 13 July 2016
Line 6:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=UNL:UNKNOWN+LIGAND'>UNL</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='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=4xyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyd OCA], [http://pdbe.org/4xyd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xyd RCSB], [http://www.ebi.ac.uk/pdbsum/4xyd 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=4xyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyd OCA], [http://pdbe.org/4xyd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xyd RCSB], [http://www.ebi.ac.uk/pdbsum/4xyd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xyd ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:33, 1 June 2016

2016-06-01T07:33:46Z

←Older revision		Revision as of 07:33, 1 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4xyd is ~~ON HOLD until Paper~~ Publication	+	==Nitric oxide reductase from Roseobacter denitrificans (RdNOR)==
		+	<StructureSection load='4xyd' size='340' side='right' caption='[[4xyd]], [[Resolution\|resolution]] 2.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xyd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Roseobacter_denitrificans_(strain_atcc_33942_/_och_114) Roseobacter denitrificans (strain atcc 33942 / och 114)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XYD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=UNL:UNKNOWN+LIGAND'>UNL</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xyd OCA], [http://pdbe.org/4xyd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xyd RCSB], [http://www.ebi.ac.uk/pdbsum/4xyd PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Membrane-intrinsic nitric oxide reductases (NORs) are key components of bacterial denitrification pathways with a close evolutionary relationship to the cytochrome oxidase (COX) complex found in aerobic respiratory chains. A key distinction between COX and NOR is the identity of the metal directly opposite the heme b3 within the active site. In NOR, this metal is iron (FeB) whereas in COX it is copper (CuB). The purified NOR of Roseobacter denitrificans contains copper and has modest oxidase activity raising the possibility that a COX-like active site might have independently arisen within the context of a NOR-like protein scaffold. Here we present the crystal structure of the Roseobacter denitrificans NorBC complex and anomalous scattering experiments probing the identity of each metal centre. Our results refute the hypothesis that copper occupies the active site and instead reveal a new metal centre in the small subunit not seen in any other NOR or COX.

-	~~Authors:~~ Crow, A.	+	Structure of the membrane-intrinsic nitric oxide reductase from Roseobacter denitrificans.,Crow A, Matsuda Y, Arata H, Oubrie A Biochemistry. 2016 May 17. PMID:27185533<ref>PMID:27185533</ref>

-	~~Description: Structure~~ of the ~~copper-containing nitric oxide reductase from Roseobacter denitrificans (RdNOR)~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 4xyd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Crow, A]]		[[Category: Crow, A]]
		+	[[Category: Heme copper oxidase superfamily]]
		+	[[Category: Membrane protein]]
		+	[[Category: Nitric oxide reductase]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "4xyd" [edit=sysop:move=sysop]

2015-02-12T10:51:49Z

Protected "4xyd" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:51, 12 February 2015

OCA: New page: '''Unreleased structure''' The entry 4xyd is ON HOLD until Paper Publication Authors: Crow, A. Description: Structure of the copper-containing nitric oxide reductase from Roseobacter d...

2015-02-12T10:51:48Z

New page: '''Unreleased structure''' The entry 4xyd is ON HOLD until Paper Publication Authors: Crow, A. Description: Structure of the copper-containing nitric oxide reductase from Roseobacter d...

New page

'''Unreleased structure'''

The entry 4xyd is ON HOLD until Paper Publication

Authors: Crow, A.

Description: Structure of the copper-containing nitric oxide reductase from Roseobacter denitrificans (RdNOR).
[[Category: Unreleased Structures]]
[[Category: Crow, A]]