5bpj - Revision history

OCA at 11:16, 10 January 2024

OCA — Wed, 10 Jan 2024 11:16:41 GMT

←Older revision		Revision as of 11:16, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bpj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Beroe_abyssicola Beroe abyssicola]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BPJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bpj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Beroe_abyssicola Beroe abyssicola]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BPJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 1.756Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5bpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpj OCA], [https://pdbe.org/5bpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bpj RCSB], [https://www.ebi.ac.uk/pdbsum/5bpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpj 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=5bpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpj OCA], [https://pdbe.org/5bpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bpj RCSB], [https://www.ebi.ac.uk/pdbsum/5bpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpj ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:02, 7 June 2023

OCA — Wed, 07 Jun 2023 06:02:50 GMT

←Older revision		Revision as of 06:02, 7 June 2023
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	<StructureSection load='5bpj' size='340' side='right'caption='[[5bpj]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='5bpj' size='340' side='right'caption='[[5bpj]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bpj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Berab Berab~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5BPJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bpj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Beroe_abyssicola Beroe abyssicola]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BPJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mn0\|4mn0]]</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=5bpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpj OCA], [https://pdbe.org/5bpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bpj RCSB], [https://www.ebi.ac.uk/pdbsum/5bpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpj ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BA2, BA1, BA3, BA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320166 BERAB])~~</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=5bpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpj OCA], [~~http~~://pdbe.org/5bpj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5bpj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5bpj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpj ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/H8ZZK1_BERAB H8ZZK1_BERAB]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Berab~~]]	+	[[Category: Beroe abyssicola]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Burakova~~, L P~~]]	+	[[Category: Burakova LP]]
-	[[Category: Liu, Z J]]	+	[[Category: Liu Z-J]]
-	[[Category: Malikova~~, N P~~]]	+	[[Category: Malikova NP]]
-	[[Category: Natashin~~, P V~~]]	+	[[Category: Natashin PV]]
-	[[Category: Niu, F]]	+	[[Category: Niu F]]
-	[[Category: Vysotski~~, E S]]~~	+	[[Category: Vysotski ES]]
-	~~[[Category: Berovin]]~~	+
-	~~[[Category: Bioluminescent protein]]~~	+
-	~~[[Category: Calcium binding]]~~	+
-	~~[[Category: Coelenterazine]]~~	+
-	~~[[Category: Coelenterazine binding]]~~	+
-	~~[[Category: Ef-hand]]~~	+
-	~~[[Category: Luminescent protein~~]]	+

OCA at 08:53, 11 March 2020

OCA — Wed, 11 Mar 2020 08:53:24 GMT

←Older revision		Revision as of 08:53, 11 March 2020
Line 1:		Line 1:

	==All Three Ca(2+)-binding Loops of Light-sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: The Spatial Structure of Mg(2+)-loaded Apo-berovin==		==All Three Ca(2+)-binding Loops of Light-sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: The Spatial Structure of Mg(2+)-loaded Apo-berovin==
-	<StructureSection load='5bpj' size='340' side='right' caption='[[5bpj]], [[Resolution\|resolution]] 1.76Å' scene=''>	+	<StructureSection load='5bpj' size='340' side='right'caption='[[5bpj]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bpj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BPJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bpj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Berab Berab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BPJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mn0\|4mn0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mn0\|4mn0]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BA2, BA1, BA3, BA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320166 BERAB])</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=5bpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpj OCA], [http://pdbe.org/5bpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bpj RCSB], [http://www.ebi.ac.uk/pdbsum/5bpj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpj 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=5bpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpj OCA], [http://pdbe.org/5bpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bpj RCSB], [http://www.ebi.ac.uk/pdbsum/5bpj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpj ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Berab]]
		+	[[Category: Large Structures]]
	[[Category: Burakova, L P]]		[[Category: Burakova, L P]]
	[[Category: Liu, Z J]]		[[Category: Liu, Z J]]

OCA at 06:53, 26 July 2016

OCA — Tue, 26 Jul 2016 06:53:21 GMT

←Older revision		Revision as of 06:53, 26 July 2016
Line 1:		Line 1:
		+
	==All Three Ca(2+)-binding Loops of Light-sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: The Spatial Structure of Mg(2+)-loaded Apo-berovin==		==All Three Ca(2+)-binding Loops of Light-sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: The Spatial Structure of Mg(2+)-loaded Apo-berovin==
	<StructureSection load='5bpj' size='340' side='right' caption='[[5bpj]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='5bpj' size='340' side='right' caption='[[5bpj]], [[Resolution\|resolution]] 1.76Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mn0\|4mn0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mn0\|4mn0]]</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=5bpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpj OCA], [http://pdbe.org/5bpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bpj RCSB], [http://www.ebi.ac.uk/pdbsum/5bpj 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=5bpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpj OCA], [http://pdbe.org/5bpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bpj RCSB], [http://www.ebi.ac.uk/pdbsum/5bpj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpj ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Light-sensitive photoprotein berovin accounts for a bright bioluminescence of ctenophore Beroe abyssicola. Berovin is functionally identical to the well-studied Ca(2+)-regulated photoproteins of jellyfish, however in contrast to those it is extremely sensitive to the visible light. Berovin contains three EF-hand Ca(2+)-binding sites and consequently belongs to a large family of the EF-hand Ca(2+)-binding proteins. Here we report the spatial structure of apo-berovin with bound Mg(2+) determined at 1.75A. The magnesium ion is found in each functional EF-hand loop of a photoprotein and coordinated by oxygen atoms donated by the side-chain groups of aspartate, carbonyl groups of the peptide backbone, or hydroxyl group of serine with characteristic oxygen-Mg(2+) distances. As oxygen supplied by the side-chain of the twelfth residue of all Ca(2+)-binding loops participates in the magnesium ion coordination, it was suggested that Ca(2+)-binding loops of berovin belong to the mixed Ca(2+)/Mg(2+) rather than Ca(2+)-specific type. In addition, we report an effect of physiological concentration of Mg(2+) on bioluminescence of berovin (sensitivity to Ca(2+), rapid-mixed kinetics, light-sensitivity, thermostability, and apo-berovin conversion into active protein). The different impact of physiological concentration of Mg(2+) on berovin bioluminescence as compared to hydromedusan photoproteins was attributed to different affinities of the Ca(2+)-binding sites of these photoproteins to Mg(2+).
		+
		+	All Ca(2+)-binding loops of light-sensitive ctenophore photoprotein berovin bind magnesium ions: The spatial structure of Mg(2+)-loaded apo-berovin.,Burakova LP, Natashin PV, Malikova NP, Niu F, Pu M, Vysotski ES, Liu ZJ J Photochem Photobiol B. 2016 Jan;154:57-66. doi:, 10.1016/j.jphotobiol.2015.11.012. Epub 2015 Dec 2. PMID:26690016<ref>PMID:26690016</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5bpj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:37, 30 December 2015

OCA — Wed, 30 Dec 2015 19:37:05 GMT

←Older revision		Revision as of 19:37, 30 December 2015
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	==All Three Ca(2+)-binding Loops of Light-sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: The Spatial Structure of Mg(2+)-loaded Apo-berovin==
-		+	<StructureSection load='5bpj' size='340' side='right' caption='[[5bpj]], [[Resolution\|resolution]] 1.76Å' scene=''>
-	~~The entry 5bpj is ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5bpj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BPJ FirstGlance]. <br>
-	~~Authors: Burakova, L.P., Natashin, P.V., Malikova, N.P., Niu, F., Vysotski, E.S., Liu, Z.-J.~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mn0\|4mn0]]</td></tr>
-	~~Description:~~ All Three Ca(2+)-binding Loops of Light-sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: The Spatial Structure of Mg(2+)-loaded Apo-berovin	+	<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=5bpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpj OCA], [http://pdbe.org/5bpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bpj RCSB], [http://www.ebi.ac.uk/pdbsum/5bpj PDBsum]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Liu~~, Z.-J]]	+	__TOC__
-	[[Category: ~~Vysotski~~, ~~E.S~~]]	+	</StructureSection>
-	[[Category: Malikova, N.P]]	+	[[Category: Burakova, L P]]
-	[[Category: ~~Burakova~~, L.P]]	+	[[Category: Liu, Z J]]
		+	[[Category: Malikova, N P]]
		+	[[Category: Natashin, P V]]
	[[Category: Niu, F]]		[[Category: Niu, F]]
-	[[Category: ~~Natashin~~, ~~P.V~~]]	+	[[Category: Vysotski, E S]]
		+	[[Category: Berovin]]
		+	[[Category: Bioluminescent protein]]
		+	[[Category: Calcium binding]]
		+	[[Category: Coelenterazine]]
		+	[[Category: Coelenterazine binding]]
		+	[[Category: Ef-hand]]
		+	[[Category: Luminescent protein]]

OCA at 10:08, 16 December 2015

OCA — Wed, 16 Dec 2015 10:08:30 GMT

←Older revision		Revision as of 10:08, 16 December 2015
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	Description: All Three Ca(2+)-binding Loops of Light-sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: The Spatial Structure of Mg(2+)-loaded Apo-berovin		Description: All Three Ca(2+)-binding Loops of Light-sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: The Spatial Structure of Mg(2+)-loaded Apo-berovin
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Malikova, N.P]]
-	[[Category: Burakova, L.P]]
	[[Category: Liu, Z.-J]]		[[Category: Liu, Z.-J]]
	[[Category: Vysotski, E.S]]		[[Category: Vysotski, E.S]]
		+	[[Category: Malikova, N.P]]
		+	[[Category: Burakova, L.P]]
	[[Category: Niu, F]]		[[Category: Niu, F]]
	[[Category: Natashin, P.V]]		[[Category: Natashin, P.V]]

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

OCA — Wed, 03 Jun 2015 11:46:07 GMT

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

←Older revision

Revision as of 11:46, 3 June 2015

OCA: New page: '''Unreleased structure''' The entry 5bpj is ON HOLD Authors: Burakova, L.P., Natashin, P.V., Malikova, N.P., Niu, F., Vysotski, E.S., Liu, Z.-J. Description: All Three Ca(2+)-binding ...

OCA — Wed, 03 Jun 2015 11:46:06 GMT

New page: '''Unreleased structure''' The entry 5bpj is ON HOLD Authors: Burakova, L.P., Natashin, P.V., Malikova, N.P., Niu, F., Vysotski, E.S., Liu, Z.-J. Description: All Three Ca(2+)-binding ...

New page

'''Unreleased structure'''

The entry 5bpj is ON HOLD

Authors: Burakova, L.P., Natashin, P.V., Malikova, N.P., Niu, F., Vysotski, E.S., Liu, Z.-J.

Description: All Three Ca(2+)-binding Loops of Light-sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: The Spatial Structure of Mg(2+)-loaded Apo-berovin
[[Category: Unreleased Structures]]
[[Category: Malikova, N.P]]
[[Category: Burakova, L.P]]
[[Category: Liu, Z.-J]]
[[Category: Vysotski, E.S]]
[[Category: Niu, F]]
[[Category: Natashin, P.V]]