5zab - Revision history

OCA at 08:50, 22 November 2023

OCA — Wed, 22 Nov 2023 08:50:38 GMT

←Older revision		Revision as of 08:50, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5zab' size='340' side='right'caption='[[5zab]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5zab' size='340' side='right'caption='[[5zab]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zab]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aeqvi Aeqvi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZAB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zab]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZAB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9A3:(2S)-8-benzyl-2-hydroperoxy-6-(4-hydroxyphenyl)-2-{[4-(trifluoromethyl)phenyl]methyl}imidazo[1,2-a]pyrazin-3(2H)-one'>9A3</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]] 2.147Å</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=5zab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zab OCA], [~~http~~://pdbe.org/5zab PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zab RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zab PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zab ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9A3:(2S)-8-benzyl-2-hydroperoxy-6-(4-hydroxyphenyl)-2-{[4-(trifluoromethyl)phenyl]methyl}imidazo[1,2-a]pyrazin-3(2H)-one'>9A3</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=5zab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zab OCA], [https://pdbe.org/5zab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zab RCSB], [https://www.ebi.ac.uk/pdbsum/5zab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zab ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AEQ2_AEQVI AEQ2_AEQVI]] Ca(2+)-dependent bioluminescence photoprotein. Displays an emission peak at 470 nm (blue light). Trace amounts of calcium ion trigger the intramolecular oxidation of the chromophore, coelenterazine into coelenteramide and CO(2) with the concomitant emission of light.	+	[https://www.uniprot.org/uniprot/AEQ2_AEQVI AEQ2_AEQVI] Ca(2+)-dependent bioluminescence photoprotein. Displays an emission peak at 470 nm (blue light). Trace amounts of calcium ion trigger the intramolecular oxidation of the chromophore, coelenterazine into coelenteramide and CO(2) with the concomitant emission of light.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aeqvi~~]]	+	[[Category: Aequorea victoria]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hosoya, T]]	+	[[Category: Hosoya T]]
-	[[Category: Inouye, S]]	+	[[Category: Inouye S]]
-	[[Category: Sekine~~, S I~~]]	+	[[Category: Sekine SI]]
-	[[Category: Shirouzu, M]]	+	[[Category: Shirouzu M]]
-	[[Category: Tomabechi, Y]]	+	[[Category: Tomabechi Y]]
-	~~[[Category: Luminescent protein]]~~	+
-	~~[[Category: Semi-synthetic aequorin~~]]	+

OCA at 21:17, 28 October 2020

OCA — Wed, 28 Oct 2020 21:17:22 GMT

←Older revision		Revision as of 21:17, 28 October 2020
Line 1:		Line 1:

	==Crystal structure of cf3-aequorin==		==Crystal structure of cf3-aequorin==
-	<StructureSection load='5zab' size='340' side='right' caption='[[5zab]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='5zab' size='340' side='right'caption='[[5zab]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zab]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeqvi Aeqvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZAB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zab]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeqvi Aeqvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZAB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9A3:(2S)-8-benzyl-2-hydroperoxy-6-(4-hydroxyphenyl)-2-{[4-(trifluoromethyl)phenyl]methyl}imidazo[1,2-a]pyrazin-3(2H)-one'>9A3</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9A3:(2S)-8-benzyl-2-hydroperoxy-6-(4-hydroxyphenyl)-2-{[4-(trifluoromethyl)phenyl]methyl}imidazo[1,2-a]pyrazin-3(2H)-one'>9A3</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=5zab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zab OCA], [http://pdbe.org/5zab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zab RCSB], [http://www.ebi.ac.uk/pdbsum/5zab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zab 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=5zab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zab OCA], [http://pdbe.org/5zab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zab RCSB], [http://www.ebi.ac.uk/pdbsum/5zab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zab ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Aeqvi]]		[[Category: Aeqvi]]
		+	[[Category: Large Structures]]
	[[Category: Hosoya, T]]		[[Category: Hosoya, T]]
	[[Category: Inouye, S]]		[[Category: Inouye, S]]

OCA at 07:53, 29 August 2018

OCA — Wed, 29 Aug 2018 07:53:26 GMT

←Older revision		Revision as of 07:53, 29 August 2018
Line 3:		Line 3:
	<StructureSection load='5zab' size='340' side='right' caption='[[5zab]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5zab' size='340' side='right' caption='[[5zab]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zab]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZAB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zab]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeqvi Aeqvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZAB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9A3:(2S)-8-benzyl-2-hydroperoxy-6-(4-hydroxyphenyl)-2-{[4-(trifluoromethyl)phenyl]methyl}imidazo[1,2-a]pyrazin-3(2H)-one'>9A3</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9A3:(2S)-8-benzyl-2-hydroperoxy-6-(4-hydroxyphenyl)-2-{[4-(trifluoromethyl)phenyl]methyl}imidazo[1,2-a]pyrazin-3(2H)-one'>9A3</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=5zab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zab OCA], [http://pdbe.org/5zab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zab RCSB], [http://www.ebi.ac.uk/pdbsum/5zab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zab 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=5zab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zab OCA], [http://pdbe.org/5zab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zab RCSB], [http://www.ebi.ac.uk/pdbsum/5zab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zab ProSAT]</span></td></tr>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aeqvi]]
	[[Category: Hosoya, T]]		[[Category: Hosoya, T]]
	[[Category: Inouye, S]]		[[Category: Inouye, S]]

OCA at 05:53, 6 June 2018

OCA — Wed, 06 Jun 2018 05:53:58 GMT

←Older revision		Revision as of 05:53, 6 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zab is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of cf3-aequorin==
		+	<StructureSection load='5zab' size='340' side='right' caption='[[5zab]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zab]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZAB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9A3:(2S)-8-benzyl-2-hydroperoxy-6-(4-hydroxyphenyl)-2-{[4-(trifluoromethyl)phenyl]methyl}imidazo[1,2-a]pyrazin-3(2H)-one'>9A3</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=5zab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zab OCA], [http://pdbe.org/5zab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zab RCSB], [http://www.ebi.ac.uk/pdbsum/5zab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zab ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AEQ2_AEQVI AEQ2_AEQVI]] Ca(2+)-dependent bioluminescence photoprotein. Displays an emission peak at 470 nm (blue light). Trace amounts of calcium ion trigger the intramolecular oxidation of the chromophore, coelenterazine into coelenteramide and CO(2) with the concomitant emission of light.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	cf3-Aequorin is one of the semi-synthetic aequorins that was produced by replacing 2-peroxycoelenterazine (CTZ-OOH) in native aequorin with a 2-peroxycoelenterazine analog, and it was prepared using the C2-modified trifluoromethyl analog of coelenterazine (cf3-CTZ) and the histidine-tagged apoaequorin expressed in Escherichia coli cells. The purified cf3-aequorin showed a slow luminescence pattern with half-decay time of Imax of 5.0 s. This is much longer than that of 0.9 s for native aequorin, and its luminescence capacity was estimated to be 72.8% of that of native aequorin. The crystal structure of cf3-aequorin was determined at 2.15 A resolution. The light source of 2-peroxytrifluoromethylcoelenterazine (cf3-CTZ-OOH) was stabilized by the hydrogen-bonding interactions at the C2-peroxy moiety and the p-hydroxy moiety at the C6-phenyl group. In native aequorin, three water molecules contribute to stabilizing CTZ-OOH through hydrogen bonds. However, cf3-aequorin only contained one water molecule, and the trifluoromethyl moiety at the C2-benzyl group of cf3-CTZ-OOH interacted with the protein by van der Waals interactions. The slow luminescence kinetics of cf3-aequorin could be explained by slow conformational changes due to the bulkiness of the trifluoromethyl group, which might hinder the smooth cleavage of hydrogen bonds at the C2-peroxy moiety after the binding of Ca2+ to cf3-aequorin.

-	~~Authors~~:	+	Slow luminescence kinetics of semi-synthetic aequorin: Expression, purification and structure determination of cf3-aequorin.,Inouye S, Tomabechi Y, Hosoya T, Sekine SI, Shirouzu M J Biochem. 2018 May 23. pii: 5001758. doi: 10.1093/jb/mvy049. PMID:29796619<ref>PMID:29796619</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5zab" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hosoya, T]]
		+	[[Category: Inouye, S]]
		+	[[Category: Sekine, S I]]
		+	[[Category: Shirouzu, M]]
		+	[[Category: Tomabechi, Y]]
		+	[[Category: Luminescent protein]]
		+	[[Category: Semi-synthetic aequorin]]

OCA at 04:57, 14 March 2018

OCA — Wed, 14 Mar 2018 04:57:47 GMT

←Older revision		Revision as of 04:57, 14 March 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Thu, 15 Feb 2018 05:11:45 GMT

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

←Older revision

Revision as of 05:11, 15 February 2018

OCA: New page: '''Unreleased structure''' The entry 5zab is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 15 Feb 2018 05:11:44 GMT

New page: '''Unreleased structure''' The entry 5zab is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5zab is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]