5fvb - Revision history

OCA at 13:28, 26 July 2023

2023-07-26T13:28:18Z

← Older revision		Revision as of 13:28, 26 July 2023
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	<StructureSection load='5fvb' size='340' side='right'caption='[[5fvb]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='5fvb' size='340' side='right'caption='[[5fvb]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5fvb]] is a 24 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Phormidium_rubidum~~ Phormidium rubidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[5fvb]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Phormidium_rubidum_A09DM Phormidium rubidum A09DM]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FVB 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=PEB:PHYCOERYTHROBILIN'>PEB</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]] 1.93Å</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MEN:N-METHYL+ASPARAGINE'>MEN</scene>, <scene name='pdbligand=PEB:PHYCOERYTHROBILIN'>PEB</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=5fvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvb OCA], [~~http~~://pdbe.org/5fvb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fvb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fvb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvb 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=5fvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvb OCA], [https://pdbe.org/5fvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fvb RCSB], [https://www.ebi.ac.uk/pdbsum/5fvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvb ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/A0A0E3W010_9CYAN A0A0E3W010_9CYAN]
	<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: Phormidium rubidum]]		[[Category: Phormidium rubidum A09DM]]
	[[Category: Gupta~~, G D~~]]		[[Category: Gupta GD]]
	[[Category: Kumar, V]]		[[Category: Kumar V]]
	[[Category: Madamwar, D]]		[[Category: Madamwar D]]
	[[Category: Sharma, M]]		[[Category: Sharma M]]
	[[Category: Sonani~~, R R]]~~		[[Category: Sonani RR]]
	~~[[Category: C-phycoerythrin]]~~
	~~[[Category: Peb chromophore]]~~
	~~[[Category: Phormidium]]~~
	~~[[Category: Photosynthesis~~]]

OCA at 07:39, 6 May 2020

2020-05-06T07:39:06Z

← Older revision		Revision as of 07:39, 6 May 2020
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	==CRYSTAL STRUCTURE OF PHORMIDIUM C-PHYCOERYTHRIN AT PH 5.0==		==CRYSTAL STRUCTURE OF PHORMIDIUM C-PHYCOERYTHRIN AT PH 5.0==
	<StructureSection load='5fvb' size='340' side='right' caption='[[5fvb]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='5fvb' size='340' side='right'caption='[[5fvb]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5fvb]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Phormidium_rubidum Phormidium rubidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[5fvb]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Phormidium_rubidum Phormidium rubidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FVB 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=PEB:PHYCOERYTHROBILIN'>PEB</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=PEB:PHYCOERYTHROBILIN'>PEB</scene></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='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='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=5fvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvb OCA], [http://pdbe.org/5fvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fvb RCSB], [http://www.ebi.ac.uk/pdbsum/5fvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvb 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=5fvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvb OCA], [http://pdbe.org/5fvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fvb RCSB], [http://www.ebi.ac.uk/pdbsum/5fvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvb ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Phormidium rubidum]]		[[Category: Phormidium rubidum]]
	[[Category: Gupta, G D]]		[[Category: Gupta, G D]]

OCA at 10:23, 13 July 2016

2016-07-13T10:23:15Z

← Older revision		Revision as of 10:23, 13 July 2016
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	~~'''Unreleased structure'''~~

	~~The entry~~ 5fvb is ~~ON HOLD until Paper~~ Publication		==CRYSTAL STRUCTURE OF PHORMIDIUM C-PHYCOERYTHRIN AT PH 5.0==
			<StructureSection load='5fvb' size='340' side='right' caption='[[5fvb]], [[Resolution\|resolution]] 1.93Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[5fvb]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Phormidium_rubidum Phormidium rubidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FVB 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=PEB:PHYCOERYTHROBILIN'>PEB</scene></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='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=5fvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fvb OCA], [http://pdbe.org/5fvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fvb RCSB], [http://www.ebi.ac.uk/pdbsum/5fvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fvb ProSAT]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The role of unique sequence features of C-phycoerythrin, isolated from Phormidium sp. A09DM, has been investigated by crystallographic studies. Two conserved indels (i.e. inserts or deletions) are found in the beta-subunit of Phormidium phycoerythrin that are distinctive characteristics of large number of cyanobacterial sequences. The identified signatures are a two-residue deletion from position 21 and a nine-residue insertion at position 146. Crystals of Phormidium phycoerythrin were obtained at pH values of 5 and 8.5, and structures have been resolved to high precision at 1.95 and 2.1 A resolution, respectively. In both the structures, heterodimers of alpha- and beta- subunits assemble as hexamers. The 7-residue insertion at position 146 significantly reduces solvent exposure of pi-conjugated A-C rings of a phycoerythrobilin (PEB) chromophore, and can influence energy absorption and energy transfer characteristics. The structural analyses (with 12-fold redundancy) suggest that protein micro-environment alone dictates the conformation of bound chromophores. The low- and high-energy absorbing chromophores are identified based on A-B ring coplanarity. The spatial distribution of these is found to be similar to that observed in R-phycoerythrin, suggesting the direction of energy transfer from outer-surface of hexamer to inner-hollow cavity in the Phormidium protein. The crystal structures also reveal that a commonly observed Hydrogen-bonding network in phycobiliproteins, involving chromophore bound to alpha-subunit and amino acid at position 73 of beta-subunit, may not be essential for structural and functional integrity of C-phycoerythrin orthologs. In solution, the protein displays slight red shift and decrease in fluorescence emission at acidic pH. The mechanism for which may be static and correlates with the proximity of +ve electric field of Arg148 to the C-ring of a PEB chromophore.

	~~Authors:~~ Kumar, V., Sonani~~, R.R.~~, Sharma, M., Gupta, G.D., ~~Madamwar, D~~.		Crystal structure analysis of C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM.,Kumar V, Sonani RR, Sharma M, Gupta GD, Madamwar D Photosynth Res. 2016 Jul;129(1):17-28. doi: 10.1007/s11120-016-0259-5. Epub 2016 , Apr 11. PMID:27068646<ref>PMID:27068646</ref>

	~~Description~~: ~~CRYSTAL STRUCTURE OF PHORMIDIUM C-PHYCOERYTHRIN AT PH 5.0~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased Structures~~]]		</div>
			<div class="pdbe-citations 5fvb" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Phormidium rubidum]]
			[[Category: Gupta, G D]]
	[[Category: Kumar, V]]		[[Category: Kumar, V]]
	[[Category: ~~Sonani~~, ~~R.R~~]]		[[Category: Madamwar, D]]
	[[Category: Sharma, M]]		[[Category: Sharma, M]]
	[[Category: ~~Madamwar~~, D]]		[[Category: Sonani, R R]]
	[[Category: ~~Gupta, G.D~~]]		[[Category: C-phycoerythrin]]
			[[Category: Peb chromophore]]
			[[Category: Phormidium]]
			[[Category: Photosynthesis]]

OCA at 00:49, 10 March 2016

2016-03-10T00:49:06Z

← Older revision		Revision as of 00:49, 10 March 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 5fvb is ON HOLD		The entry 5fvb is ON HOLD until Paper Publication

	Authors: Kumar, V., Sonani, R.R., Sharma, M., Gupta, G.D., Madamwar, D.		Authors: Kumar, V., Sonani, R.R., Sharma, M., Gupta, G.D., Madamwar, D.

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

2016-02-26T15:36:20Z

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

← Older revision	Revision as of 15:36, 26 February 2016
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5fvb is ON HOLD Authors: Kumar, V., Sonani, R.R., Sharma, M., Gupta, G.D., Madamwar, D. Description: CRYSTAL STRUCTURE OF PHORMIDIUM C-PHYCOERYTHRI...

2016-02-26T15:36:18Z

New page: '''Unreleased structure''' The entry 5fvb is ON HOLD Authors: Kumar, V., Sonani, R.R., Sharma, M., Gupta, G.D., Madamwar, D. Description: CRYSTAL STRUCTURE OF PHORMIDIUM C-PHYCOERYTHRI...

New page

'''Unreleased structure'''

The entry 5fvb is ON HOLD

Authors: Kumar, V., Sonani, R.R., Sharma, M., Gupta, G.D., Madamwar, D.

Description: CRYSTAL STRUCTURE OF PHORMIDIUM C-PHYCOERYTHRIN AT PH 5.0
[[Category: Unreleased Structures]]
[[Category: Kumar, V]]
[[Category: Sonani, R.R]]
[[Category: Sharma, M]]
[[Category: Madamwar, D]]
[[Category: Gupta, G.D]]