5n9z - Revision history

OCA at 12:40, 15 November 2023

OCA — Wed, 15 Nov 2023 12:40:51 GMT

←Older revision		Revision as of 12:40, 15 November 2023
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	<StructureSection load='5n9z' size='340' side='right'caption='[[5n9z]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5n9z' size='340' side='right'caption='[[5n9z]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n9z]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thalassiosira_hyalina Thalassiosira hyalina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N9Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5N9Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n9z]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Thalassiosira_hyalina Thalassiosira hyalina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N9Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5N9Z FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=CAP:2~~-~~CARBOXYARABINITOL-1~~,~~5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.899Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=8RE:'>8RE</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=HLU:BETA-HYDROXYLEUCINE'>HLU</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=LYO:4-HYDROXY-LYSINE'>LYO</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8RE:3,4-dihydroxylysine'>8RE</scene>, <scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HLU:BETA-HYDROXYLEUCINE'>HLU</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=LYO:4-HYDROXY-LYSINE'>LYO</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39]~~ </~~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=5n9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n9z OCA], [https://pdbe.org/5n9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5n9z RCSB], [https://www.ebi.ac.uk/pdbsum/5n9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5n9z 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=5n9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n9z OCA], [~~http~~://pdbe.org/5n9z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5n9z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5n9z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5n9z ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A384E0M2_9STRA A0A384E0M2_9STRA]
	<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: Ribulose-bisphosphate carboxylase]]
	[[Category: Thalassiosira hyalina]]		[[Category: Thalassiosira hyalina]]
-	[[Category: Andersson, I]]	+	[[Category: Andersson I]]
-	[[Category: Valegard, K]]	+	[[Category: Valegard K]]
-	~~[[Category: Carbon dioxide fixation]]~~	+
-	~~[[Category: Photorespiration]]~~	+
-	~~[[Category: Photosynthesis~~]]	+

OCA at 07:39, 24 April 2019

OCA — Wed, 24 Apr 2019 07:39:03 GMT

←Older revision		Revision as of 07:39, 24 April 2019
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	==Rubisco from Thalassiosira hyalina==		==Rubisco from Thalassiosira hyalina==
-	<StructureSection load='5n9z' size='340' side='right' caption='[[5n9z]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5n9z' size='340' side='right'caption='[[5n9z]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5n9z]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Thalassiosira_hyalina Thalassiosira hyalina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N9Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[5n9z]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Thalassiosira_hyalina Thalassiosira hyalina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N9Z FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ribulose-bisphosphate carboxylase]]		[[Category: Ribulose-bisphosphate carboxylase]]
	[[Category: Thalassiosira hyalina]]		[[Category: Thalassiosira hyalina]]

OCA at 10:20, 5 September 2018

OCA — Wed, 05 Sep 2018 10:20:34 GMT

←Older revision		Revision as of 10:20, 5 September 2018
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	<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=5n9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n9z OCA], [http://pdbe.org/5n9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n9z RCSB], [http://www.ebi.ac.uk/pdbsum/5n9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n9z 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=5n9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n9z OCA], [http://pdbe.org/5n9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n9z RCSB], [http://www.ebi.ac.uk/pdbsum/5n9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n9z ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The catalytic performance of the major CO2-assimilating enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), restricts photosynthetic productivity. Natural diversity in the catalytic properties of Rubisco indicates possibilities for improvement. Oceanic phytoplankton contain some of the most efficient Rubisco enzymes, and diatoms in particular are responsible for a significant proportion of total marine primary production as well as being a major source of CO2 sequestration in polar cold waters. Until now, the biochemical properties and three-dimensional structures of Rubisco from diatoms were unknown. Here, diatoms from Arctic waters were collected, cultivated and analyzed for their CO2 fixing capability. We characterized the kinetic properties of five, and determined the crystal structures of four Rubiscos selected for their high CO2-fixing efficiency. The DNA sequences of the rbcL and rbcS genes of the selected diatoms were similar, reflecting their close phylogenetic relationship. The Vmax and KM for the oxygenase and carboxylase activities at 25 degrees C and the specificity factors (Sc/o) at 15, 25 and 35 degrees C, were determined. The Sc/o values were high, approaching those of mono- and dicot plants, thus exhibiting good selectivity for CO2 relative to O2 Structurally, diatom Rubiscos belong to Form I C/D, containing small subunits characterised by a short betaA-betaB loop and a carboxy-terminal extension that forms a beta-hairpin structure (betaE-betaF loop). Of note, the diatom Rubiscos featured a number of posttranslational modifications of the large subunit, including 4-hydroxy-proline, betahydroxyleucine, hydroxylated, and nitrosylated cysteine, mono-, and di-hydroxylated lysine, and tri-methylated lysine. Our studies suggest adaptation toward achieving efficient CO2-fixation in Arctic diatom Rubiscos.
		+
		+	Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications.,Valegard K, Andralojc PJ, Haslam RP, Pearce FG, Eriksen GK, Madgwick PJ, Kristoffersen AK, van Lun M, Klein U, Eilertsen HC, Parry MAJ, Andersson I J Biol Chem. 2018 Jun 20. pii: RA118.003518. doi: 10.1074/jbc.RA118.003518. PMID:29925588<ref>PMID:29925588</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5n9z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:19, 14 March 2018

OCA — Wed, 14 Mar 2018 06:19:21 GMT

←Older revision		Revision as of 06:19, 14 March 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5n9z is ~~ON HOLD until Paper Publication~~	+	==Rubisco from Thalassiosira hyalina==
-		+	<StructureSection load='5n9z' size='340' side='right' caption='[[5n9z]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors~~: ~~Andersson~~, I., ~~Valegard~~, K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5n9z]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Thalassiosira_hyalina Thalassiosira hyalina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N9Z FirstGlance]. <br>
-	~~Description~~: ~~Rubisco from~~ Thalassiosira hyalina	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8RE:'>8RE</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=HLU:BETA-HYDROXYLEUCINE'>HLU</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=LYO:4-HYDROXY-LYSINE'>LYO</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </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=5n9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n9z OCA], [http://pdbe.org/5n9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n9z RCSB], [http://www.ebi.ac.uk/pdbsum/5n9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n9z ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ribulose-bisphosphate carboxylase]]
		+	[[Category: Thalassiosira hyalina]]
		+	[[Category: Andersson, I]]
	[[Category: Valegard, K]]		[[Category: Valegard, K]]
-	[[Category: ~~Andersson, I~~]]	+	[[Category: Carbon dioxide fixation]]
		+	[[Category: Photorespiration]]
		+	[[Category: Photosynthesis]]

OCA at 17:08, 24 January 2018

OCA — Wed, 24 Jan 2018 17:08:10 GMT

←Older revision		Revision as of 17:08, 24 January 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5n9z is ON HOLD	+	The entry 5n9z is ON HOLD until Paper Publication

	Authors: Andersson, I., Valegard, K.		Authors: Andersson, I., Valegard, K.

OCA at 11:23, 27 September 2017

OCA — Wed, 27 Sep 2017 11:23:56 GMT

←Older revision		Revision as of 11:23, 27 September 2017
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	Authors: Andersson, I., Valegard, K.		Authors: Andersson, I., Valegard, K.

-	Description: Rubisco from Thalassiosira ~~antartica~~	+	Description: Rubisco from Thalassiosira hyalina
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Valegard, K]]		[[Category: Valegard, K]]
	[[Category: Andersson, I]]		[[Category: Andersson, I]]

OCA: Protected "5n9z" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 12:20:22 GMT

Protected "5n9z" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:20, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5n9z is ON HOLD Authors: Andersson, I., Valegard, K. Description: Rubisco from Thalassiosira antartica Category: Unreleased Structures [[Catego...

OCA — Thu, 09 Mar 2017 12:20:21 GMT

New page: '''Unreleased structure''' The entry 5n9z is ON HOLD Authors: Andersson, I., Valegard, K. Description: Rubisco from Thalassiosira antartica Category: Unreleased Structures [[Catego...

New page

'''Unreleased structure'''

The entry 5n9z is ON HOLD

Authors: Andersson, I., Valegard, K.

Description: Rubisco from Thalassiosira antartica
[[Category: Unreleased Structures]]
[[Category: Valegard, K]]
[[Category: Andersson, I]]