6m9b - Revision history

OCA at 14:41, 13 March 2024

OCA — Wed, 13 Mar 2024 14:41:48 GMT

←Older revision		Revision as of 14:41, 13 March 2024
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	<StructureSection load='6m9b' size='340' side='right'caption='[[6m9b]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='6m9b' size='340' side='right'caption='[[6m9b]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m9b]] 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=6M9B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6M9B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m9b]] 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=6M9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M9B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTN:BIOTIN'>BTN</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]] 1.548Å</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=6m9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m9b OCA], [~~http~~://pdbe.org/6m9b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6m9b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6m9b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6m9b ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTN:BIOTIN'>BTN</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=6m9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m9b OCA], [https://pdbe.org/6m9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m9b RCSB], [https://www.ebi.ac.uk/pdbsum/6m9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m9b 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;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Native single-wavelength anomalous dispersion (SAD) is the most attractive de novo phasing method in macromolecular crystallography, as it directly utilizes intrinsic anomalous scattering from native crystals. However, the success of such an experiment depends on accurate measurements of the reflection intensities and therefore on careful data-collection protocols. Here, the low-dose, multiple-orientation data-collection protocol for native SAD phasing developed at beamline X06DA (PXIII) at the Swiss Light Source is reviewed, and its usage over the last four years on conventional crystals (>50 microm) is reported. Being experimentally very simple and fast, this method has gained popularity and has delivered 45 de novo structures to date (13 of which have been published). Native SAD is currently the primary choice for experimental phasing among X06DA users. The method can address challenging cases: here, native SAD phasing performed on a streptavidin-biotin crystal with P21 symmetry and a low Bijvoet ratio of 0.6% is highlighted. The use of intrinsic anomalous signals as sequence markers for model building and the assignment of ions is also briefly described.	+

-	Making routine native SAD a reality: lessons from beamline X06DA at the Swiss Light Source.,Basu S, Finke A, Vera L, Wang M, Olieric V Acta Crystallogr D Struct Biol. 2019 Mar 1;75(Pt 3):262-271. doi:, 10.1107/S2059798319003103. Epub 2019 Mar 12. PMID:30950397<ref>PMID:30950397</ref>	+	==See Also==
-		+	*[[Avidin 3D structures\|Avidin 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6m9b" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: As 4 1583]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Finke, A D~~]]	+	[[Category: Streptomyces avidinii]]
-	[[Category: ~~Biotin binder]]~~	+	[[Category: Finke AD]]
-	~~[[Category: Ligand]]~~	+
-	~~[[Category: Structural protein]]~~	+
-	~~[[Category: Tetramer]]~~	+
-	~~[[Category: Wild type~~]]	+

OCA at 11:37, 13 November 2019

OCA — Wed, 13 Nov 2019 11:37:34 GMT

←Older revision		Revision as of 11:37, 13 November 2019
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	<StructureSection load='6m9b' size='340' side='right'caption='[[6m9b]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='6m9b' size='340' side='right'caption='[[6m9b]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m9b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M9B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m9b]] 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=6M9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M9B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTN:BIOTIN'>BTN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTN:BIOTIN'>BTN</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=6m9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m9b OCA], [http://pdbe.org/6m9b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m9b RCSB], [http://www.ebi.ac.uk/pdbsum/6m9b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m9b 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=6m9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m9b OCA], [http://pdbe.org/6m9b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m9b RCSB], [http://www.ebi.ac.uk/pdbsum/6m9b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m9b ProSAT]</span></td></tr>
Line 9:		Line 9:
	== 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).		[[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 ==
		+	Native single-wavelength anomalous dispersion (SAD) is the most attractive de novo phasing method in macromolecular crystallography, as it directly utilizes intrinsic anomalous scattering from native crystals. However, the success of such an experiment depends on accurate measurements of the reflection intensities and therefore on careful data-collection protocols. Here, the low-dose, multiple-orientation data-collection protocol for native SAD phasing developed at beamline X06DA (PXIII) at the Swiss Light Source is reviewed, and its usage over the last four years on conventional crystals (>50 microm) is reported. Being experimentally very simple and fast, this method has gained popularity and has delivered 45 de novo structures to date (13 of which have been published). Native SAD is currently the primary choice for experimental phasing among X06DA users. The method can address challenging cases: here, native SAD phasing performed on a streptavidin-biotin crystal with P21 symmetry and a low Bijvoet ratio of 0.6% is highlighted. The use of intrinsic anomalous signals as sequence markers for model building and the assignment of ions is also briefly described.
		+
		+	Making routine native SAD a reality: lessons from beamline X06DA at the Swiss Light Source.,Basu S, Finke A, Vera L, Wang M, Olieric V Acta Crystallogr D Struct Biol. 2019 Mar 1;75(Pt 3):262-271. doi:, 10.1107/S2059798319003103. Epub 2019 Mar 12. PMID:30950397<ref>PMID:30950397</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6m9b" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: As 4 1583]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Finke, A D]]		[[Category: Finke, A D]]

OCA at 06:01, 17 April 2019

OCA — Wed, 17 Apr 2019 06:01:28 GMT

←Older revision		Revision as of 06:01, 17 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6m9b is ON HOLD until Paper Publication~~	+	==Wild-type streptavidin in complex with biotin solved by native SAD with data collected at 6 keV==
-		+	<StructureSection load='6m9b' size='340' side='right'caption='[[6m9b]], [[Resolution\|resolution]] 1.55Å' scene=''>
-	~~Authors: Finke, A.D.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6m9b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M9B FirstGlance]. <br>
-	~~Description:~~ Wild-type streptavidin in complex with biotin solved by native SAD with data collected at 6 keV	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTN:BIOTIN'>BTN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6m9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m9b OCA], [http://pdbe.org/6m9b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m9b RCSB], [http://www.ebi.ac.uk/pdbsum/6m9b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m9b ProSAT]</span></td></tr>
-	[[Category: Finke, A.D]]	+	</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).
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Finke, A D]]
		+	[[Category: Biotin binder]]
		+	[[Category: Ligand]]
		+	[[Category: Structural protein]]
		+	[[Category: Tetramer]]
		+	[[Category: Wild type]]

OCA at 08:50, 5 September 2018

OCA — Wed, 05 Sep 2018 08:50:50 GMT

←Older revision		Revision as of 08:50, 5 September 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6m9b is ON HOLD	+	The entry 6m9b is ON HOLD until Paper Publication

	Authors: Finke, A.D.		Authors: Finke, A.D.

OCA: Protected "6m9b" [edit=sysop:move=sysop]

OCA — Wed, 29 Aug 2018 06:09:14 GMT

Protected "6m9b" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:09, 29 August 2018

OCA: New page: '''Unreleased structure''' The entry 6m9b is ON HOLD Authors: Finke, A.D. Description: Wild-type streptavidin in complex with biotin solved by native SAD with data collected at 6 keV [...

OCA — Wed, 29 Aug 2018 06:09:13 GMT

New page: '''Unreleased structure''' The entry 6m9b is ON HOLD Authors: Finke, A.D. Description: Wild-type streptavidin in complex with biotin solved by native SAD with data collected at 6 keV [...

New page

'''Unreleased structure'''

The entry 6m9b is ON HOLD

Authors: Finke, A.D.

Description: Wild-type streptavidin in complex with biotin solved by native SAD with data collected at 6 keV
[[Category: Unreleased Structures]]
[[Category: Finke, A.D]]