4jnj - Revision history

OCA at 11:25, 24 November 2022

OCA — Thu, 24 Nov 2022 11:25:44 GMT

←Older revision		Revision as of 11:25, 24 November 2022
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	<StructureSection load='4jnj' size='340' side='right'caption='[[4jnj]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4jnj' size='340' side='right'caption='[[4jnj]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jnj]] 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=4JNJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4JNJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jnj]] 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=4JNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JNJ 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4jnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jnj OCA], [~~http~~://pdbe.org/4jnj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4jnj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4jnj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4jnj 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=4jnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jnj OCA], [https://pdbe.org/4jnj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jnj RCSB], [https://www.ebi.ac.uk/pdbsum/4jnj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jnj ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: As 4 1583]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: DeMonte, D]]	+	[[Category: Streptomyces avidinii]]
-	[[Category: Drake~~, E J~~]]	+	[[Category: DeMonte D]]
-	[[Category: Gulick~~, A M~~]]	+	[[Category: Drake EJ]]
-	[[Category: Lim, K ~~Hong~~]]	+	[[Category: Gulick AM]]
-	[[Category: Park, S]]	+	[[Category: Hong Lim K]]
-	~~[[Category: Beta barrel]]~~	+	[[Category: Park S]]
-	~~[[Category: Biotin]]~~	+
-	~~[[Category: Biotin-binding protein]]~~	+
-	~~[[Category: Engineered streptavidin variant]]~~	+
-	~~[[Category: Protein binding~~]]	+

OCA at 09:29, 3 April 2019

OCA — Wed, 03 Apr 2019 09:29:39 GMT

←Older revision		Revision as of 09:29, 3 April 2019
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	==Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate==		==Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate==
-	<StructureSection load='4jnj' size='340' side='right' caption='[[4jnj]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4jnj' size='340' side='right'caption='[[4jnj]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4jnj]] 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=4JNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JNJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4jnj]] 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=4JNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JNJ FirstGlance]. <br>
Line 18:		Line 18:

	==See Also==		==See Also==
-	*[[Avidin\|Avidin]]	+	*[[Avidin 3D structures\|Avidin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: As 4 1583]]		[[Category: As 4 1583]]
		+	[[Category: Large Structures]]
	[[Category: DeMonte, D]]		[[Category: DeMonte, D]]
	[[Category: Drake, E J]]		[[Category: Drake, E J]]

OCA at 08:07, 4 August 2016

OCA — Thu, 04 Aug 2016 08:07:27 GMT

←Older revision		Revision as of 08:07, 4 August 2016
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		+
	==Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate==		==Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate==
	<StructureSection load='4jnj' size='340' side='right' caption='[[4jnj]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4jnj' size='340' side='right' caption='[[4jnj]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4jnj]] 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=4JNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JNJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4jnj]] 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=4JNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JNJ 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4jnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jnj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jnj RCSB], [http://www.ebi.ac.uk/pdbsum/4jnj PDBsum]</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=4jnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jnj OCA], [http://pdbe.org/4jnj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jnj RCSB], [http://www.ebi.ac.uk/pdbsum/4jnj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jnj ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4jnj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 14:56, 21 December 2014

OCA — Sun, 21 Dec 2014 14:56:04 GMT

←Older revision		Revision as of 14:56, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4jnj\| PDB=4jnj \| SCENE= }}~~	+	==Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate==
-	===Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate===	+	<StructureSection load='4jnj' size='340' side='right' caption='[[4jnj]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23670729}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4jnj]] 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=4JNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JNJ 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4jnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jnj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jnj RCSB], [http://www.ebi.ac.uk/pdbsum/4jnj PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We recently reported the engineering of monomeric streptavidin, mSA, corresponding to a single subunit of wild type (wt) streptavidin tetramer. The monomer was designed by homology modeling, in which the streptavidin and rhizavidin sequences were combined to engineer a high affinity binding pocket containing residues from a single subunit only. Although mSA is stable and binds biotin with nanomolar affinity, its fast off rate (koff ) creates practical challenges during applications. We obtained a 1.9 A crystal structure of mSA bound to biotin to understand their interaction in detail, and used the structure to introduce targeted mutations to improve its binding kinetics. F43 of shwanavidin forms a hydrophobic lid that is important for biotin binding. However, the T48F mutation in mSA, which introduces a comparable hydrophobic lid only results in a modest 20 - 40% improvement in the measured koff . On the other hand, introducing the S25H mutation near the bicyclic ring of bound biotin increases the dissociation half life (t(1/2) ) from 11 min to 83 min at 20 degrees C. Molecular dynamics (MD) simulations suggest that H25 stabilizes the binding loop L3,4 by interacting with A47, and protects key intermolecular hydrogen bonds by limiting solvent entry into the binding pocket. Concurrent T48F or T48W mutation clashes with H25 and partially abrogates the beneficial effects of H25. Taken together, this study suggests that stabilization of the binding loop and solvation of the binding pocket are important determinants of the dissociation kinetics in mSA. (c) Proteins 2013;. (c) 2013 Wiley Periodicals, Inc.

-	~~==About this~~ Structure==	+	Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate.,Demonte D, Drake EJ, Lim KH, Gulick AM, Park S Proteins. 2013 May 13. doi: 10.1002/prot.24320. PMID:23670729<ref>PMID:23670729</ref>
-	~~[[4jnj]] 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=4JNJ OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Avidin\|Avidin]]		*[[Avidin\|Avidin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023670729</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: As 4 1583]]		[[Category: As 4 1583]]
-	[[Category: DeMonte, D.]]	+	[[Category: DeMonte, D]]
-	[[Category: Drake, E J.]]	+	[[Category: Drake, E J]]
-	[[Category: Gulick, A M.]]	+	[[Category: Gulick, A M]]
-	[[Category: Lim, K Hong.]]	+	[[Category: Lim, K Hong]]
-	[[Category: Park, S.]]	+	[[Category: Park, S]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Biotin]]		[[Category: Biotin]]

OCA at 06:55, 13 November 2013

OCA — Wed, 13 Nov 2013 06:55:06 GMT

←Older revision		Revision as of 06:55, 13 November 2013
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	==About this Structure==		==About this Structure==
-	[[4jnj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_avidinii Streptomyces avidinii~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JNJ OCA].	+	[[4jnj]] 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=4JNJ OCA].
		+
		+	==See Also==
		+	*[[Avidin\|Avidin]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:023670729</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:023670729</ref><references group="xtra"/><references/>
-	[[Category: ~~Streptomyces avidinii~~]]	+	[[Category: As 4 1583]]
	[[Category: DeMonte, D.]]		[[Category: DeMonte, D.]]
	[[Category: Drake, E J.]]		[[Category: Drake, E J.]]

OCA at 16:21, 19 June 2013

OCA — Wed, 19 Jun 2013 16:21:52 GMT

←Older revision		Revision as of 16:21, 19 June 2013
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-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4jnj\| PDB=4jnj \| SCENE= }}
		+	===Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate===
		+	{{ABSTRACT_PUBMED_23670729}}

-	~~The entry~~ 4jnj is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4jnj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avidinii Streptomyces avidinii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JNJ OCA].

-	~~Authors~~: DeMonte, D., Drake, E.J.~~, Hong Lim, K.,~~ Gulick, A.M., Park, S.	+	==Reference==
-		+	<ref group="xtra">PMID:023670729</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Structure based engineering of~~ streptavidin ~~monomer with a reduced biotin dissociation rate~~	+	[[Category: Streptomyces avidinii]]
		+	[[Category: DeMonte, D.]]
		+	[[Category: Drake, E J.]]
		+	[[Category: Gulick, A M.]]
		+	[[Category: Lim, K Hong.]]
		+	[[Category: Park, S.]]
		+	[[Category: Beta barrel]]
		+	[[Category: Biotin]]
		+	[[Category: Biotin-binding protein]]
		+	[[Category: Engineered streptavidin variant]]
		+	[[Category: Protein binding]]

OCA at 10:54, 24 April 2013

OCA — Wed, 24 Apr 2013 10:54:41 GMT

←Older revision		Revision as of 10:54, 24 April 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4jnj is ON HOLD	+	The entry 4jnj is ON HOLD until Paper Publication

	Authors: DeMonte, D., Drake, E.J., Hong Lim, K., Gulick, A.M., Park, S.		Authors: DeMonte, D., Drake, E.J., Hong Lim, K., Gulick, A.M., Park, S.

	Description: Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate		Description: Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate

OCA at 19:56, 17 April 2013

OCA — Wed, 17 Apr 2013 19:56:45 GMT

←Older revision		Revision as of 19:56, 17 April 2013
Line 3:		Line 3:
	The entry 4jnj is ON HOLD		The entry 4jnj is ON HOLD

-	Authors: ~~Daniel~~ DeMonte, ~~Eric J~~ Drake, ~~Kok~~ Hong Lim, ~~Andrew M~~ Gulick, ~~Sheldon~~ Park	+	Authors: DeMonte, D., Drake, E.J., Hong Lim, K., Gulick, A.M., Park, S.

	Description: Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate		Description: Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate

OCA: Protected "4jnj" [edit=sysop:move=sysop]

OCA — Wed, 27 Mar 2013 08:19:25 GMT

Protected "4jnj" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:19, 27 March 2013

OCA: New page: '''Unreleased structure''' The entry 4jnj is ON HOLD Authors: Daniel DeMonte, Eric J Drake, Kok Hong Lim, Andrew M Gulick, Sheldon Park Description: Structure based engineering of stre...

OCA — Wed, 27 Mar 2013 08:19:24 GMT

New page: '''Unreleased structure''' The entry 4jnj is ON HOLD Authors: Daniel DeMonte, Eric J Drake, Kok Hong Lim, Andrew M Gulick, Sheldon Park Description: Structure based engineering of stre...

New page

'''Unreleased structure'''

The entry 4jnj is ON HOLD

Authors: Daniel DeMonte, Eric J Drake, Kok Hong Lim, Andrew M Gulick, Sheldon Park

Description: Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate