7r36 - Revision history

OCA at 13:25, 1 February 2024

OCA — Thu, 01 Feb 2024 13:25:41 GMT

←Older revision		Revision as of 13:25, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7r36]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlorella_variabilis Chlorella variabilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7R36 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7R36 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7r36]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlorella_variabilis Chlorella variabilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7R36 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7R36 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=STE:STEARIC+ACID'>STE</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]] 2.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=STE:STEARIC+ACID'>STE</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=7r36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7r36 OCA], [https://pdbe.org/7r36 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7r36 RCSB], [https://www.ebi.ac.uk/pdbsum/7r36 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7r36 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=7r36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7r36 OCA], [https://pdbe.org/7r36 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7r36 RCSB], [https://www.ebi.ac.uk/pdbsum/7r36 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7r36 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/FAP_CHLVA FAP_CHLVA]] Catalyzes the decarboxylation of free fatty acids to n-alkanes or n-alkenes in response to blue light (PubMed:28860382, PubMed:30106504, PubMed:30673222). Substrate preference is toward fatty acids with C16 or C17 chains (PubMed:28860382, PubMed:30106504, PubMed:30673222). Saturated fatty acids are converted to alkanes, not alkenes (PubMed:28860382). The decarboxylation is initiated through electron abstraction from the fatty acid by the photo-excited FAD (PubMed:28860382).<ref>PMID:28860382</ref> <ref>PMID:30106504</ref> <ref>PMID:30673222</ref>	+	[https://www.uniprot.org/uniprot/FAP_CHLVA FAP_CHLVA] Catalyzes the decarboxylation of free fatty acids to n-alkanes or n-alkenes in response to blue light (PubMed:28860382, PubMed:30106504, PubMed:30673222). Substrate preference is toward fatty acids with C16 or C17 chains (PubMed:28860382, PubMed:30106504, PubMed:30673222). Saturated fatty acids are converted to alkanes, not alkenes (PubMed:28860382). The decarboxylation is initiated through electron abstraction from the fatty acid by the photo-excited FAD (PubMed:28860382).<ref>PMID:28860382</ref> <ref>PMID:30106504</ref> <ref>PMID:30673222</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 06:54, 14 September 2022

OCA — Wed, 14 Sep 2022 06:54:09 GMT

←Older revision		Revision as of 06:54, 14 September 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7r36 is ~~ON HOLD until Paper~~ Publication	+	==Difference-refined structure of fatty acid photodecarboxylase 2 microsecond following 400-nm laser irradiation of the dark-state determined by SFX==
		+	<StructureSection load='7r36' size='340' side='right'caption='[[7r36]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7r36]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlorella_variabilis Chlorella variabilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7R36 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7R36 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=STE:STEARIC+ACID'>STE</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=7r36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7r36 OCA], [https://pdbe.org/7r36 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7r36 RCSB], [https://www.ebi.ac.uk/pdbsum/7r36 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7r36 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/FAP_CHLVA FAP_CHLVA]] Catalyzes the decarboxylation of free fatty acids to n-alkanes or n-alkenes in response to blue light (PubMed:28860382, PubMed:30106504, PubMed:30673222). Substrate preference is toward fatty acids with C16 or C17 chains (PubMed:28860382, PubMed:30106504, PubMed:30673222). Saturated fatty acids are converted to alkanes, not alkenes (PubMed:28860382). The decarboxylation is initiated through electron abstraction from the fatty acid by the photo-excited FAD (PubMed:28860382).<ref>PMID:28860382</ref> <ref>PMID:30106504</ref> <ref>PMID:30673222</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Upon absorption of a blue-light photon, fatty-acid photodecarboxylase catalyzes the decarboxylation of free fatty acids to form hydrocarbons (for example alkanes or alkenes). The major components of the catalytic mechanism have recently been elucidated by combining static and time-resolved serial femtosecond crystallography (TR-SFX), time-resolved vibrational and electronic spectroscopies, quantum-chemical calculations and site-directed mutagenesis [Sorigue et al. (2021), Science, 372, eabd5687]. The TR-SFX experiments, which were carried out at four different picosecond to microsecond pump-probe delays, yielded input for the calculation of Fourier difference maps that demonstrated light-induced decarboxylation. Here, some of the difficulties encountered during the experiment as well as during data processing are highlighted, in particular regarding space-group assignment, a pump-laser power titration is described and data analysis is extended by structure-factor extrapolation of the TR-SFX data. Structure refinement against extrapolated structure factors reveals a reorientation of the generated hydrocarbon and the formation of a photoproduct close to Cys432 and Arg451. Identification of its chemical nature, CO2 or bicarbonate, was not possible because of the limited data quality, which was assigned to specificities of the crystalline system. Further TR-SFX experiments on a different crystal form are required to identify the photoproducts and their movements during the catalytic cycle.

-	~~Authors~~: ~~Hadjidemetriou~~, K., Coquelle, N., Barends~~, T.R.M.~~, De Zitter, E., Schlichting, I., Colletier, J.P., ~~Weik, M~~.	+	Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned.,Hadjidemetriou K, Coquelle N, Barends TRM, De Zitter E, Schlichting I, Colletier JP, Weik M Acta Crystallogr D Struct Biol. 2022 Sep 1;78(Pt 9):1131-1142. doi:, 10.1107/S2059798322007525. Epub 2022 Aug 25. PMID:36048153<ref>PMID:36048153</ref>

-	~~Description: Difference-refined structure of fatty acid photodecarboxylase 2 microsecond following 400-nm laser irradiation~~ of the ~~dark~~-~~state determined by SFX~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Schlichting, I~~]]	+	<div class="pdbe-citations 7r36" style="background-color:#fffaf0;"></div>
-	[[Category: Barends~~, T.R.M~~]]	+	== References ==
-	[[Category: Colletier~~, J.P~~]]	+	<references/>
-	[[Category: ~~Hadjidemetriou, K~~]]	+	__TOC__
-	[[Category: ~~Weik, M~~]]	+	</StructureSection>
-	[[Category: ~~De Zitter, E~~]]	+	[[Category: Chlorella variabilis]]
-	[[Category: ~~Coquelle, N~~]]	+	[[Category: Large Structures]]
		+	[[Category: Barends TRM]]
		+	[[Category: Colletier JP]]
		+	[[Category: Coquelle N]]
		+	[[Category: De Zitter E]]
		+	[[Category: Hadjidemetriou K]]
		+	[[Category: Schlichting I]]
		+	[[Category: Weik M]]

OCA at 16:17, 27 July 2022

OCA — Wed, 27 Jul 2022 16:17:48 GMT

←Older revision		Revision as of 16:17, 27 July 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7r36 is ON HOLD	+	The entry 7r36 is ON HOLD until Paper Publication

	Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, M.		Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, M.
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	Description: Difference-refined structure of fatty acid photodecarboxylase 2 microsecond following 400-nm laser irradiation of the dark-state determined by SFX		Description: Difference-refined structure of fatty acid photodecarboxylase 2 microsecond following 400-nm laser irradiation of the dark-state determined by SFX
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Hadjidemetriou, K]]
-	[[Category: De Zitter, E]]
-	[[Category: Coquelle, N]]
	[[Category: Schlichting, I]]		[[Category: Schlichting, I]]
	[[Category: Barends, T.R.M]]		[[Category: Barends, T.R.M]]
	[[Category: Colletier, J.P]]		[[Category: Colletier, J.P]]
		+	[[Category: Hadjidemetriou, K]]
	[[Category: Weik, M]]		[[Category: Weik, M]]
		+	[[Category: De Zitter, E]]
		+	[[Category: Coquelle, N]]

OCA at 06:03, 29 June 2022

OCA — Wed, 29 Jun 2022 06:03:03 GMT

←Older revision		Revision as of 06:03, 29 June 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7r36 is ON HOLD ~~until sometime in the future~~	+	The entry 7r36 is ON HOLD

	Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, M.		Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, M.

OCA at 10:20, 27 April 2022

OCA — Wed, 27 Apr 2022 10:20:57 GMT

←Older revision		Revision as of 10:20, 27 April 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7r36 is ON HOLD until ~~Paper Publication~~	+	The entry 7r36 is ON HOLD until sometime in the future

	Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, M.		Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, M.

OCA at 09:44, 23 March 2022

OCA — Wed, 23 Mar 2022 09:44:42 GMT

←Older revision		Revision as of 09:44, 23 March 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7r36 is ON HOLD	+	The entry 7r36 is ON HOLD until Paper Publication

	Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, M.		Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, M.

OCA at 05:00, 2 March 2022

OCA — Wed, 02 Mar 2022 05:00:19 GMT

←Older revision		Revision as of 05:00, 2 March 2022
Line 3:		Line 3:
	The entry 7r36 is ON HOLD		The entry 7r36 is ON HOLD

-	Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, W.	+	Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, M.

	Description: Difference-refined structure of fatty acid photodecarboxylase 2 microsecond following 400-nm laser irradiation of the dark-state determined by SFX		Description: Difference-refined structure of fatty acid photodecarboxylase 2 microsecond following 400-nm laser irradiation of the dark-state determined by SFX
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Weik, W]]
	[[Category: Hadjidemetriou, K]]		[[Category: Hadjidemetriou, K]]
	[[Category: De Zitter, E]]		[[Category: De Zitter, E]]
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	[[Category: Barends, T.R.M]]		[[Category: Barends, T.R.M]]
	[[Category: Colletier, J.P]]		[[Category: Colletier, J.P]]
		+	[[Category: Weik, M]]

OCA: Protected "7r36" [edit=sysop:move=sysop]

OCA — Wed, 16 Feb 2022 09:01:08 GMT

Protected "7r36" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:01, 16 February 2022

OCA: New page: '''Unreleased structure''' The entry 7r36 is ON HOLD Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, W. Description: ...

OCA — Wed, 16 Feb 2022 09:01:07 GMT

New page: '''Unreleased structure''' The entry 7r36 is ON HOLD Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, W. Description: ...

New page

'''Unreleased structure'''

The entry 7r36 is ON HOLD

Authors: Hadjidemetriou, K., Coquelle, N., Barends, T.R.M., De Zitter, E., Schlichting, I., Colletier, J.P., Weik, W.

Description: Difference-refined structure of fatty acid photodecarboxylase 2 microsecond following 400-nm laser irradiation of the dark-state determined by SFX
[[Category: Unreleased Structures]]
[[Category: Weik, W]]
[[Category: Hadjidemetriou, K]]
[[Category: De Zitter, E]]
[[Category: Coquelle, N]]
[[Category: Schlichting, I]]
[[Category: Barends, T.R.M]]
[[Category: Colletier, J.P]]