4rmp - Revision history

OCA at 17:52, 20 September 2023

2023-09-20T17:52:16Z

←Older revision		Revision as of 17:52, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rmp]] is a 2 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=4RMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RMP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rmp]] is a 2 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=4RMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RMP FirstGlance]. <br>
-	</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=MEN:N-METHYL+ASPARAGINE'>MEN</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]] 2.506Å</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=MEN:N-METHYL+ASPARAGINE'>MEN</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=4rmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rmp OCA], [https://pdbe.org/4rmp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rmp RCSB], [https://www.ebi.ac.uk/pdbsum/4rmp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rmp 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=4rmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rmp OCA], [https://pdbe.org/4rmp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rmp RCSB], [https://www.ebi.ac.uk/pdbsum/4rmp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rmp ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:04, 2 March 2023

2023-03-02T07:04:54Z

←Older revision		Revision as of 07:04, 2 March 2023
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	<StructureSection load='4rmp' size='340' side='right'caption='[[4rmp]], [[Resolution\|resolution]] 2.51Å' scene=''>		<StructureSection load='4rmp' size='340' side='right'caption='[[4rmp]], [[Resolution\|resolution]] 2.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rmp]] is a 2 chain structure with sequence from [~~http~~://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=4RMP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RMP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rmp]] is a 2 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=4RMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RMP 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>~~</td></tr>~~	+	</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=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'>[https://proteopedia.org/fgij/fg.htm?mol=4rmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rmp OCA], [https://pdbe.org/4rmp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rmp RCSB], [https://www.ebi.ac.uk/pdbsum/4rmp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rmp 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=4rmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rmp OCA], [~~http~~://pdbe.org/4rmp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rmp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rmp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rmp ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A078K1U6_9CYAN A0A078K1U6_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 ~~a09dm~~]]	+	[[Category: Phormidium rubidum A09DM]]
-	[[Category: Gupta~~, G D~~]]	+	[[Category: Gupta GD]]
-	[[Category: Kumar, V]]	+	[[Category: Kumar V]]
-	[[Category: Madamwar, D]]	+	[[Category: Madamwar D]]
-	[[Category: Sonani~~, R R]]~~	+	[[Category: Sonani RR]]
-	~~[[Category: Light harvesting phycobiliprotein]]~~	+
-	~~[[Category: Photosynthesis]]~~	+
-	~~[[Category: Phycocyanobilin chromophore~~]]	+

OCA at 10:36, 1 May 2019

2019-05-01T10:36:41Z

←Older revision		Revision as of 10:36, 1 May 2019
Line 1:		Line 1:

	==Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM==		==Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM==
-	<StructureSection load='4rmp' size='340' side='right' caption='[[4rmp]], [[Resolution\|resolution]] 2.51Å' scene=''>	+	<StructureSection load='4rmp' size='340' side='right'caption='[[4rmp]], [[Resolution\|resolution]] 2.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rmp]] is a 2 chain structure with sequence from [http://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=4RMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RMP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rmp]] is a 2 chain structure with sequence from [http://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=4RMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RMP FirstGlance]. <br>
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[Allophycocyanin\|Allophycocyanin]]	+	*[[Allophycocyanin 3D structures\|Allophycocyanin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Phormidium rubidum a09dm]]		[[Category: Phormidium rubidum a09dm]]
	[[Category: Gupta, G D]]		[[Category: Gupta, G D]]

OCA at 01:59, 10 March 2017

2017-03-10T01:59:03Z

←Older revision		Revision as of 01:59, 10 March 2017
Line 1:		Line 1:
		+
	==Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM==		==Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM==
	<StructureSection load='4rmp' size='340' side='right' caption='[[4rmp]], [[Resolution\|resolution]] 2.51Å' scene=''>		<StructureSection load='4rmp' size='340' side='right' caption='[[4rmp]], [[Resolution\|resolution]] 2.51Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</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=4rmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rmp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rmp RCSB], [http://www.ebi.ac.uk/pdbsum/4rmp 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=4rmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rmp OCA], [http://pdbe.org/4rmp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rmp RCSB], [http://www.ebi.ac.uk/pdbsum/4rmp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rmp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4rmp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Allophycocyanin\|Allophycocyanin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:18, 13 May 2015

2015-05-13T12:18:29Z

←Older revision		Revision as of 12:18, 13 May 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM==
		+	<StructureSection load='4rmp' size='340' side='right' caption='[[4rmp]], [[Resolution\|resolution]] 2.51Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4rmp]] is a 2 chain structure with sequence from [http://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=4RMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RMP 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></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=4rmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rmp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rmp RCSB], [http://www.ebi.ac.uk/pdbsum/4rmp PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Isolated phycobilisome (PBS) sub-assemblies have been widely subjected to X-ray crystallography analysis to obtain greater insights into the structure-function relationship of this light harvesting complex. Allophycocyanin (APC) is the phycobiliprotein always found in the PBS core complex. Phycocyanobilin (PCB) chromophores, covalently bound to conserved Cys residues of alpha- and beta- subunits of APC, are responsible for solar energy absorption from phycocyanin and for transfer to photosynthetic apparatus. In the known APC structures, heterodimers of alpha- and beta- subunits (known as alphabeta monomers) assemble as trimer or hexamer. We here for the first time report the crystal structure of APC isolated from a marine cyanobacterium (Phormidium sp. A09DM). The crystal structure has been refined against all the observed data to the resolution of 2.51 A to Rwork (Rfree) of 0.158 (0.229) with good stereochemistry of the atomic model. The Phormidium protein exists as a trimer of alphabeta monomers in solution and in crystal lattice. The overall tertiary structures of alpha- and beta- subunits, and trimeric quaternary fold of the Phormidium protein resemble the other known APC structures. Also, configuration and conformation of the two covalently bound PCB chromophores in the marine APC are same as those observed in fresh water cyanobacteria and marine red algae. More hydrophobic residues, however, constitute the environment of the chromophore bound to alpha-subunit of the Phormidium protein, owing mainly to amino acid substitutions in the marine protein.

-	~~The entry 4rmp is ON HOLD until Paper Publication~~	+	Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM.,Sonani RR, Gupta GD, Madamwar D, Kumar V PLoS One. 2015 Apr 29;10(4):e0124580. doi: 10.1371/journal.pone.0124580., eCollection 2015. PMID:25923120<ref>PMID:25923120</ref>

-	~~Authors: Kumar~~, V.~~, Gupta, G~~.~~D., Sonani, R.R., Madamwar, D~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of allophycocyanin from marine cyanobacterium~~ Phormidium ~~sp. A09DM~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Phormidium rubidum a09dm]]
		+	[[Category: Gupta, G D]]
	[[Category: Kumar, V]]		[[Category: Kumar, V]]
-	[[Category: Sonani, R.R]]
	[[Category: Madamwar, D]]		[[Category: Madamwar, D]]
-	[[Category: ~~Gupta~~, ~~G.D~~]]	+	[[Category: Sonani, R R]]
		+	[[Category: Light harvesting phycobiliprotein]]
		+	[[Category: Photosynthesis]]
		+	[[Category: Phycocyanobilin chromophore]]

OCA at 17:03, 24 December 2014

2014-12-24T17:03:58Z

←Older revision		Revision as of 17:03, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM		Description: Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM
		+	[[Category: Unreleased Structures]]
		+	[[Category: Kumar, V]]
		+	[[Category: Sonani, R.R]]
		+	[[Category: Madamwar, D]]
		+	[[Category: Gupta, G.D]]

OCA at 06:43, 26 November 2014

2014-11-26T06:43:45Z

←Older revision		Revision as of 06:43, 26 November 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4rmp is ON HOLD	+	The entry 4rmp is ON HOLD until Paper Publication

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

	Description: Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM		Description: Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM

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

2014-10-29T10:10:06Z

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

←Older revision

Revision as of 10:10, 29 October 2014

OCA: New page: '''Unreleased structure''' The entry 4rmp is ON HOLD Authors: Kumar, V., Gupta, G.D., Sonani, R.R., Madamwar, D. Description: Crystal structure of allophycocyanin from marine cyanobact...

2014-10-29T10:10:05Z

New page: '''Unreleased structure''' The entry 4rmp is ON HOLD Authors: Kumar, V., Gupta, G.D., Sonani, R.R., Madamwar, D. Description: Crystal structure of allophycocyanin from marine cyanobact...

New page

'''Unreleased structure'''

The entry 4rmp is ON HOLD

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

Description: Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM