5jd2 - Revision history

OCA at 12:36, 6 March 2024

OCA — Wed, 06 Mar 2024 12:36:55 GMT

←Older revision		Revision as of 12:36, 6 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/SAV_STRAV SAV_STRAV] The biological function of streptavidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of streptavidin).		[https://www.uniprot.org/uniprot/SAV_STRAV SAV_STRAV] The biological function of streptavidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of streptavidin).
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity and wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.
-
-	Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser.,Hunter MS, Yoon CH, DeMirci H, Sierra RG, Dao EH, Ahmadi R, Aksit F, Aquila AL, Ciftci H, Guillet S, Hayes MJ, Lane TJ, Liang M, Lundstrom U, Koglin JE, Mgbam P, Rao Y, Zhang L, Wakatsuki S, Holton JM, Boutet S Nat Commun. 2016 Nov 4;7:13388. doi: 10.1038/ncomms13388. PMID:27811937<ref>PMID:27811937</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5jd2" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Avidin 3D structures\|Avidin 3D structures]]		*[[Avidin 3D structures\|Avidin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:59, 6 September 2023

OCA — Wed, 06 Sep 2023 10:59:24 GMT

←Older revision		Revision as of 10:59, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='5jd2' size='340' side='right'caption='[[5jd2]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5jd2' size='340' side='right'caption='[[5jd2]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jd2]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~As_4.1583 As 4.1583~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JD2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JD2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jd2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avidinii Streptomyces avidinii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JD2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BYY:5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-SELENOPHENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC+ACID'>BYY</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]] 1.9Å</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=5jd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jd2 OCA], [~~http~~://pdbe.org/5jd2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jd2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jd2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jd2 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BYY:5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-SELENOPHENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC+ACID'>BYY</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=5jd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jd2 OCA], [https://pdbe.org/5jd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jd2 RCSB], [https://www.ebi.ac.uk/pdbsum/5jd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jd2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SAV_STRAV SAV_STRAV]] The biological function of streptavidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of streptavidin).	+	[https://www.uniprot.org/uniprot/SAV_STRAV SAV_STRAV] The biological function of streptavidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of streptavidin).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: As 4 1583]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Boutet, S~~]]	+	[[Category: Streptomyces avidinii]]
-	[[Category: ~~DeMirci, H]]~~	+	[[Category: Boutet S]]
-	~~[[Category: Hunter, M~~ S]]	+	[[Category: DeMirci H]]
-	[[Category: ~~Biotin binding protein~~]]	+	[[Category: Hunter MS]]
-	[[Category: ~~Fel]]~~	+
-	~~[[Category: Sad]]~~	+
-	~~[[Category: Sfx]]~~	+
-	~~[[Category: Streptavidin~~]]	+

OCA at 09:09, 4 December 2019

OCA — Wed, 04 Dec 2019 09:09:25 GMT

←Older revision		Revision as of 09:09, 4 December 2019
Line 1:		Line 1:

	==SFX structure of corestreptavidin-selenobiotin complex==		==SFX structure of corestreptavidin-selenobiotin complex==
-	<StructureSection load='5jd2' size='340' side='right' caption='[[5jd2]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5jd2' size='340' side='right'caption='[[5jd2]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jd2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1583 As 4.1583]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JD2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jd2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1583 As 4.1583]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JD2 FirstGlance]. <br>
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5jd2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jd2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Avidin 3D structures\|Avidin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: As 4 1583]]		[[Category: As 4 1583]]
		+	[[Category: Large Structures]]
	[[Category: Boutet, S]]		[[Category: Boutet, S]]
	[[Category: DeMirci, H]]		[[Category: DeMirci, H]]

OCA at 10:03, 22 November 2017

OCA — Wed, 22 Nov 2017 10:03:15 GMT

←Older revision		Revision as of 10:03, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='5jd2' size='340' side='right' caption='[[5jd2]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5jd2' size='340' side='right' caption='[[5jd2]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jd2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JD2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jd2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1583 As 4.1583]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JD2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BYY:5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-SELENOPHENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC+ACID'>BYY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BYY:5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-SELENOPHENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC+ACID'>BYY</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=5jd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jd2 OCA], [http://pdbe.org/5jd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jd2 RCSB], [http://www.ebi.ac.uk/pdbsum/5jd2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jd2 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=5jd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jd2 OCA], [http://pdbe.org/5jd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jd2 RCSB], [http://www.ebi.ac.uk/pdbsum/5jd2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jd2 ProSAT]</span></td></tr>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: As 4 1583]]
	[[Category: Boutet, S]]		[[Category: Boutet, S]]
	[[Category: DeMirci, H]]		[[Category: DeMirci, H]]

OCA at 03:27, 10 December 2016

OCA — Sat, 10 Dec 2016 03:27:27 GMT

←Older revision		Revision as of 03:27, 10 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jd2 is ~~ON HOLD until Paper~~ Publication	+	==SFX structure of corestreptavidin-selenobiotin complex==
		+	<StructureSection load='5jd2' size='340' side='right' caption='[[5jd2]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jd2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JD2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BYY:5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-SELENOPHENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC+ACID'>BYY</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=5jd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jd2 OCA], [http://pdbe.org/5jd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jd2 RCSB], [http://www.ebi.ac.uk/pdbsum/5jd2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jd2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SAV_STRAV SAV_STRAV]] The biological function of streptavidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of streptavidin).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity and wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.

-	~~Authors~~:	+	Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser.,Hunter MS, Yoon CH, DeMirci H, Sierra RG, Dao EH, Ahmadi R, Aksit F, Aquila AL, Ciftci H, Guillet S, Hayes MJ, Lane TJ, Liang M, Lundstrom U, Koglin JE, Mgbam P, Rao Y, Zhang L, Wakatsuki S, Holton JM, Boutet S Nat Commun. 2016 Nov 4;7:13388. doi: 10.1038/ncomms13388. PMID:27811937<ref>PMID:27811937</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5jd2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Boutet, S]]
		+	[[Category: DeMirci, H]]
		+	[[Category: Hunter, M S]]
		+	[[Category: Biotin binding protein]]
		+	[[Category: Fel]]
		+	[[Category: Sad]]
		+	[[Category: Sfx]]
		+	[[Category: Streptavidin]]

OCA at 11:18, 26 July 2016

OCA — Tue, 26 Jul 2016 11:18:10 GMT

←Older revision		Revision as of 11:18, 26 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jd2 is ON HOLD	+	The entry 5jd2 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 15:18, 15 May 2016

OCA — Sun, 15 May 2016 15:18:15 GMT

←Older revision		Revision as of 15:18, 15 May 2016
Line 3:		Line 3:
	The entry 5jd2 is ON HOLD		The entry 5jd2 is ON HOLD

-	Authors: ~~DeMirci, H., Hunter, M.S., Boutet, S.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Hunter, M.S]]
-	[[Category: Boutet, S]]
-	[[Category: Demirci, H]]

OCA: Protected "5jd2" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:52:59 GMT

Protected "5jd2" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:52, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jd2 is ON HOLD Authors: DeMirci, H., Hunter, M.S., Boutet, S. Description: Category: Unreleased Structures Category: Hunter, M.S [[Catego...

OCA — Wed, 11 May 2016 01:52:57 GMT

New page: '''Unreleased structure''' The entry 5jd2 is ON HOLD Authors: DeMirci, H., Hunter, M.S., Boutet, S. Description: Category: Unreleased Structures Category: Hunter, M.S [[Catego...

New page

'''Unreleased structure'''

The entry 5jd2 is ON HOLD

Authors: DeMirci, H., Hunter, M.S., Boutet, S.

Description:
[[Category: Unreleased Structures]]
[[Category: Hunter, M.S]]
[[Category: Boutet, S]]
[[Category: Demirci, H]]