6jpr - Revision history

OCA at 10:18, 22 November 2023

OCA — Wed, 22 Nov 2023 10:18:10 GMT

←Older revision		Revision as of 10:18, 22 November 2023
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	<StructureSection load='6jpr' size='340' side='right'caption='[[6jpr]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='6jpr' size='340' side='right'caption='[[6jpr]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jpr]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Nostoc Nostoc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JPR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JPR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jpr]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Nostoc Nostoc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JPR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene~~>, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.35Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MEN:N-METHYL+ASPARAGINE'>MEN</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MEN:N-METHYL+ASPARAGINE'>MEN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=6jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jpr OCA], [~~http~~://pdbe.org/6jpr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jpr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jpr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jpr 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=6jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jpr OCA], [https://pdbe.org/6jpr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jpr RCSB], [https://www.ebi.ac.uk/pdbsum/6jpr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jpr ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A5H1ZR40_9NOSO A0A5H1ZR40_9NOSO] Light-harvesting photosynthetic bile pigment-protein from the phycobiliprotein complex (phycobilisome, PBS). Phycocyanin is the major phycobiliprotein in the PBS rod.[ARBA:ARBA00003579]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6jpr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6jpr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phycocyanin\|Phycocyanin]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Nostoc]]		[[Category: Nostoc]]
-	[[Category: Gupta~~, G D~~]]	+	[[Category: Gupta GD]]
-	[[Category: Kumar, V]]	+	[[Category: Kumar V]]
-	[[Category: Madamwar, D]]	+	[[Category: Madamwar D]]
-	[[Category: Patel~~, S N~~]]	+	[[Category: Patel SN]]
-	[[Category: Rastogi~~, R P~~]]	+	[[Category: Rastogi RP]]
-	[[Category: Sonani~~, R R]]~~	+	[[Category: Sonani RR]]
-	~~[[Category: Cyanobacteria]]~~	+
-	~~[[Category: Light harvesting]]~~	+
-	~~[[Category: Photosynthesis]]~~	+
-	~~[[Category: Phycobiliprotein]]~~	+
-	~~[[Category: Phycocyanobilin~~]]	+

OCA at 08:37, 24 July 2019

OCA — Wed, 24 Jul 2019 08:37:26 GMT

←Older revision		Revision as of 08:37, 24 July 2019
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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=6jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jpr OCA], [http://pdbe.org/6jpr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jpr RCSB], [http://www.ebi.ac.uk/pdbsum/6jpr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jpr 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=6jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jpr OCA], [http://pdbe.org/6jpr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jpr RCSB], [http://www.ebi.ac.uk/pdbsum/6jpr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jpr ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The distinct sequence feature and spectral blue-shift (~10 nm) of phycocyanin, isolated from Nostoc sp. R76DM (N-PC), were investigated by phylogenetic and crystallographic analyses. Twelve conserved substitutions in N-PC sequence were found distributed unequally among alpha- and beta-subunit (3 in alpha- and 9 in beta-subunit). The phylogenetic analysis suggested that molecular evolution of alpha- and beta-subunit of Nostoc-phycocyanin is faster than evolution of Nostoc-species. The divergence events seem to have occurred more frequently in beta-subunit, compared to alpha-subunit (relative divergence, 7.38 for alpha-subunit and 9.66 for beta-subunit). Crystal structure of N-PC was solved at 2.35 A resolution to reasonable R-factors (Rwork/RFree = 0.199/0.248). Substitutions congregate near interface of two alphabeta-monomer in N-PC trimer and are of compensatory nature. Six of the substitutions in beta-subunit may be involved in maintaining topology of beta-subunit, one in inter-monomer interaction and one in interaction with linker-protein. The beta153Cys-attached chromophore adopts high-energy conformational state resulting due to reduced coplanarity of B- and C-pyrrole rings. Distortion in chromophore conformation can result in blue-shift in N-PC spectral properties. N-PC showed significant in-vitro and in-vivo antioxidant activity comparable with other phycocyanin. Since Nostoc-species constitute a distinct phylogenetic clade, the present structure would provide a better template to build a model for phycocyanins of these species.
		+
		+	Phylogenetic and crystallographic analysis of Nostoc phycocyanin having blue-shifted spectral properties.,Sonani RR, Rastogi RP, Patel SN, Chaubey MG, Singh NK, Gupta GD, Kumar V, Madamwar D Sci Rep. 2019 Jul 8;9(1):9863. doi: 10.1038/s41598-019-46288-4. PMID:31285455<ref>PMID:31285455</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6jpr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:53, 26 June 2019

OCA — Wed, 26 Jun 2019 06:53:57 GMT

←Older revision		Revision as of 06:53, 26 June 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6jpr ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of Phycocyanin from Nostoc sp. R76DM==
-		+	<StructureSection load='6jpr' size='340' side='right'caption='[[6jpr]], [[Resolution\|resolution]] 2.35Å' scene=''>
-	~~Authors~~: ~~Sonani, R~~.R., ~~Gupta~~, G.D., ~~Rastogi, R~~.P., ~~Patel~~, S.N., ~~Madamwar, D~~., ~~Kumar, V~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6jpr]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Nostoc Nostoc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JPR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JPR FirstGlance]. <br>
-	~~Description: Crystal structure of Phycocyanin from Nostoc sp. R76DM~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=MEN:N-METHYL+ASPARAGINE'>MEN</scene></td></tr>
-	[[Category: ~~Patel, S.N~~]]	+	<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=6jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jpr OCA], [http://pdbe.org/6jpr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jpr RCSB], [http://www.ebi.ac.uk/pdbsum/6jpr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jpr ProSAT]</span></td></tr>
-	[[Category: ~~Rastogi~~, ~~R.P~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Nostoc]]
		+	[[Category: Gupta, G D]]
	[[Category: Kumar, V]]		[[Category: Kumar, V]]
-	[[Category: Gupta, G.D]]
-	[[Category: Sonani, R.R]]
	[[Category: Madamwar, D]]		[[Category: Madamwar, D]]
		+	[[Category: Patel, S N]]
		+	[[Category: Rastogi, R P]]
		+	[[Category: Sonani, R R]]
		+	[[Category: Cyanobacteria]]
		+	[[Category: Light harvesting]]
		+	[[Category: Photosynthesis]]
		+	[[Category: Phycobiliprotein]]
		+	[[Category: Phycocyanobilin]]

OCA at 05:21, 10 April 2019

OCA — Wed, 10 Apr 2019 05:21:00 GMT

←Older revision		Revision as of 05:21, 10 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6jpr is ON HOLD	+	The entry 6jpr is ON HOLD until Paper Publication

	Authors: Sonani, R.R., Gupta, G.D., Rastogi, R.P., Patel, S.N., Madamwar, D., Kumar, V.		Authors: Sonani, R.R., Gupta, G.D., Rastogi, R.P., Patel, S.N., Madamwar, D., Kumar, V.

OCA: Protected "6jpr" [edit=sysop:move=sysop]

OCA — Wed, 03 Apr 2019 04:28:54 GMT

Protected "6jpr" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:28, 3 April 2019

OCA: New page: '''Unreleased structure''' The entry 6jpr is ON HOLD Authors: Sonani, R.R., Gupta, G.D., Rastogi, R.P., Patel, S.N., Madamwar, D., Kumar, V. Description: Crystal structure of Phycocyan...

OCA — Wed, 03 Apr 2019 04:28:53 GMT

New page: '''Unreleased structure''' The entry 6jpr is ON HOLD Authors: Sonani, R.R., Gupta, G.D., Rastogi, R.P., Patel, S.N., Madamwar, D., Kumar, V. Description: Crystal structure of Phycocyan...

New page

'''Unreleased structure'''

The entry 6jpr is ON HOLD

Authors: Sonani, R.R., Gupta, G.D., Rastogi, R.P., Patel, S.N., Madamwar, D., Kumar, V.

Description: Crystal structure of Phycocyanin from Nostoc sp. R76DM
[[Category: Unreleased Structures]]
[[Category: Patel, S.N]]
[[Category: Rastogi, R.P]]
[[Category: Kumar, V]]
[[Category: Gupta, G.D]]
[[Category: Sonani, R.R]]
[[Category: Madamwar, D]]