7dig - Revision history

OCA at 10:57, 23 October 2024

2024-10-23T10:57:32Z

← Older revision		Revision as of 10:57, 23 October 2024
Line 3:		Line 3:
	<StructureSection load='7dig' size='340' side='right'caption='[[7dig]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='7dig' size='340' side='right'caption='[[7dig]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7dig]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Dendronephthya_sp._SSAL-2002 Dendronephthya sp. SSAL-2002].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DIG FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DIG FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.6Å</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]] 2.6Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CR8:2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE'>CR8</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CR8:2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE'>CR8</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=7dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dig OCA], [https://pdbe.org/7dig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dig RCSB], [https://www.ebi.ac.uk/pdbsum/7dig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dig 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=7dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dig OCA], [https://pdbe.org/7dig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dig RCSB], [https://www.ebi.ac.uk/pdbsum/7dig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dig ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	~~[https://www.uniprot.org/uniprot/Q8T6U0_9CNID Q8T6U0_9CNID]~~
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Sensitive and accurate detection of specific metal ions is important for sensor development and can advance analytical science and support environmental and human medical examinations. Fluorescent proteins (FPs) can be quenched by specific metal ions and spectroscopically show a unique fluorescence-quenching sensitivity, suggesting their potential application as FP-based metal biosensors. Since the characteristics of the fluorescence quenching are difficult to predict, spectroscopic analysis of new FPs is important for the development of FP-based biosensors. Here we reported the spectroscopic and structural analysis of metal-induced fluorescence quenching of the photoconvertible fluorescent protein DendFP. The spectroscopic analysis showed that Fe(2+), Fe(3+), and Cu(2+) significantly reduced the fluorescence emission of DendFP. The metal titration experiments showed that the dissociation constants (Kd) of Fe(2+), Fe(3+), and Cu(2+) for DendFP were 24.59, 41.66, and 137.18 muM, respectively. The tetrameric interface of DendFP, which the metal ions cannot bind to, was analyzed. Structural comparison of the metal-binding sites of DendFP with those of iq-mEmerald and Dronpa suggested that quenchable DendFP has a unique metal-binding site on the beta-barrel that does not utilize the histidine pair for metal binding.

	Metal-Induced Fluorescence Quenching of Photoconvertible Fluorescent Protein DendFP.,Kim IJ, Xu Y, Nam KH Molecules. 2022 May 3;27(9). pii: molecules27092922. doi:, 10.3390/molecules27092922. PMID:35566273<ref>PMID:35566273</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7dig" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]		*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Dendronephthya sp. SSAL-2002]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Nam KH]]		[[Category: Nam KH]]

OCA at 10:55, 15 November 2023

2023-11-15T10:55:29Z

← Older revision		Revision as of 10:55, 15 November 2023
Line 3:		Line 3:
	<StructureSection load='7dig' size='340' side='right'caption='[[7dig]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='7dig' size='340' side='right'caption='[[7dig]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7dig]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DIG FirstGlance]. <br>		<table><tr><td colspan='2'>[[7dig]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Dendronephthya_sp._SSAL-2002 Dendronephthya sp. SSAL-2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DIG FirstGlance]. <br>
	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR8:2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE'>CR8</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]] 2.6Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CR8:2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE'>CR8</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=7dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dig OCA], [https://pdbe.org/7dig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dig RCSB], [https://www.ebi.ac.uk/pdbsum/7dig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dig 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=7dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dig OCA], [https://pdbe.org/7dig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dig RCSB], [https://www.ebi.ac.uk/pdbsum/7dig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dig ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q8T6U0_9CNID Q8T6U0_9CNID]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7dig" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7dig" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Dendronephthya sp. SSAL-2002]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Nam~~, K H]]~~		[[Category: Nam KH]]
	~~[[Category: Dendra]]~~
	~~[[Category: Dendronephthya]]~~
	~~[[Category: Fluorescent protein]]~~
	~~[[Category: Gfp~~]]

OCA at 09:51, 22 June 2022

2022-06-22T09:51:24Z

← Older revision		Revision as of 09:51, 22 June 2022
Line 1:		Line 1:

	==Green fluorescent protein from Dendronephthya sp. SSAL-2002==		==Green fluorescent protein from Dendronephthya sp. SSAL-2002==
	<StructureSection load='7dig' size='340' side='right'caption='[[7dig]]' scene=''>		<StructureSection load='7dig' size='340' side='right'caption='[[7dig]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DIG FirstGlance]. <br>		<table><tr><td colspan='2'>[[7dig]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DIG FirstGlance]. <br>
	</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=7dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dig OCA], [https://pdbe.org/7dig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dig RCSB], [https://www.ebi.ac.uk/pdbsum/7dig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dig ProSAT]</span></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR8:2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE'>CR8</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=7dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dig OCA], [https://pdbe.org/7dig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dig RCSB], [https://www.ebi.ac.uk/pdbsum/7dig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dig ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Sensitive and accurate detection of specific metal ions is important for sensor development and can advance analytical science and support environmental and human medical examinations. Fluorescent proteins (FPs) can be quenched by specific metal ions and spectroscopically show a unique fluorescence-quenching sensitivity, suggesting their potential application as FP-based metal biosensors. Since the characteristics of the fluorescence quenching are difficult to predict, spectroscopic analysis of new FPs is important for the development of FP-based biosensors. Here we reported the spectroscopic and structural analysis of metal-induced fluorescence quenching of the photoconvertible fluorescent protein DendFP. The spectroscopic analysis showed that Fe(2+), Fe(3+), and Cu(2+) significantly reduced the fluorescence emission of DendFP. The metal titration experiments showed that the dissociation constants (Kd) of Fe(2+), Fe(3+), and Cu(2+) for DendFP were 24.59, 41.66, and 137.18 muM, respectively. The tetrameric interface of DendFP, which the metal ions cannot bind to, was analyzed. Structural comparison of the metal-binding sites of DendFP with those of iq-mEmerald and Dronpa suggested that quenchable DendFP has a unique metal-binding site on the beta-barrel that does not utilize the histidine pair for metal binding.

			Metal-Induced Fluorescence Quenching of Photoconvertible Fluorescent Protein DendFP.,Kim IJ, Xu Y, Nam KH Molecules. 2022 May 3;27(9). pii: molecules27092922. doi:, 10.3390/molecules27092922. PMID:35566273<ref>PMID:35566273</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7dig" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Nam KH]]		[[Category: Nam, K H]]
			[[Category: Dendra]]
			[[Category: Dendronephthya]]
			[[Category: Fluorescent protein]]
			[[Category: Gfp]]

OCA at 09:54, 8 December 2021

2021-12-08T09:54:14Z

← Older revision		Revision as of 09:54, 8 December 2021
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7dig is ~~ON HOLD until Paper Publication~~		==Green fluorescent protein from Dendronephthya sp. SSAL-2002==
			<StructureSection load='7dig' size='340' side='right'caption='[[7dig]]' scene=''>
	~~Authors~~: ~~Nam~~, K.H.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DIG FirstGlance]. <br>
	~~Description~~: ~~Green fluorescent protein from Dendronephthya sp~~. ~~SSAL~~-~~2002~~		</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=7dig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dig OCA], [https://pdbe.org/7dig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dig RCSB], [https://www.ebi.ac.uk/pdbsum/7dig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dig ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: Nam~~, K.H~~]]		__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Nam KH]]

OCA at 13:13, 3 March 2021

2021-03-03T13:13:36Z

← Older revision		Revision as of 13:13, 3 March 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7dig is ON HOLD		The entry 7dig is ON HOLD until Paper Publication

	Authors: Nam, K.H.		Authors: Nam, K.H.

OCA: Protected "7dig" [edit=sysop:move=sysop]

2020-11-25T05:25:33Z

Protected "7dig" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:25, 25 November 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7dig is ON HOLD Authors: Nam, K.H. Description: Green fluorescent protein from Dendronephthya sp. SSAL-2002 Category: Unreleased Structures [[C...

2020-11-25T05:25:32Z

New page: '''Unreleased structure''' The entry 7dig is ON HOLD Authors: Nam, K.H. Description: Green fluorescent protein from Dendronephthya sp. SSAL-2002 Category: Unreleased Structures [[C...

New page

'''Unreleased structure'''

The entry 7dig is ON HOLD

Authors: Nam, K.H.

Description: Green fluorescent protein from Dendronephthya sp. SSAL-2002
[[Category: Unreleased Structures]]
[[Category: Nam, K.H]]