5aq7 - Revision history

OCA at 11:15, 10 January 2024

OCA — Wed, 10 Jan 2024 11:15:00 GMT

←Older revision		Revision as of 11:15, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5aq7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AQ7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5aq7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AQ7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</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]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</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=5aq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aq7 OCA], [https://pdbe.org/5aq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5aq7 RCSB], [https://www.ebi.ac.uk/pdbsum/5aq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5aq7 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=5aq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aq7 OCA], [https://pdbe.org/5aq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5aq7 RCSB], [https://www.ebi.ac.uk/pdbsum/5aq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5aq7 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:22, 31 May 2023

OCA — Wed, 31 May 2023 06:22:43 GMT

←Older revision		Revision as of 06:22, 31 May 2023
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	<StructureSection load='5aq7' size='340' side='right'caption='[[5aq7]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5aq7' size='340' side='right'caption='[[5aq7]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5aq7]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AQ7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5aq7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AQ7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5aq8\|5aq8]], [[5aq9\|5aq9]], [[5aqa\|5aqa]], [[5aqb\|5aqb]]~~</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=5aq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aq7 OCA], [https://pdbe.org/5aq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5aq7 RCSB], [https://www.ebi.ac.uk/pdbsum/5aq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5aq7 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=5aq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aq7 OCA], [~~http~~://pdbe.org/5aq7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5aq7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5aq7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5aq7 ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Batyuk, A]]	+	[[Category: Batyuk A]]
-	[[Category: Heberling, M]]	+	[[Category: Heberling M]]
-	[[Category: Honegger, A]]	+	[[Category: Honegger A]]
-	[[Category: Plueckthun, A]]	+	[[Category: Plueckthun A]]
-	[[Category: Wu, Y]]	+	[[Category: Wu Y]]
-	~~[[Category: Chaperone]]~~	+
-	~~[[Category: Crystallization chaperone]]~~	+
-	~~[[Category: Rigid domain fusion~~]]	+

OCA at 07:44, 3 July 2019

OCA — Wed, 03 Jul 2019 07:44:49 GMT

←Older revision		Revision as of 07:44, 3 July 2019
Line 1:		Line 1:

	==DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography==		==DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography==
-	<StructureSection load='5aq7' size='340' side='right' caption='[[5aq7]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5aq7' size='340' side='right'caption='[[5aq7]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5aq7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5aq7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AQ7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5aq8\|5aq8]], [[5aq9\|5aq9]], [[5aqa\|5aqa]], [[5aqb\|5aqb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5aq8\|5aq8]], [[5aq9\|5aq9]], [[5aqa\|5aqa]], [[5aqb\|5aqb]]</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=5aq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aq7 OCA], [http://pdbe.org/5aq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5aq7 RCSB], [http://www.ebi.ac.uk/pdbsum/5aq7 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=5aq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aq7 OCA], [http://pdbe.org/5aq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5aq7 RCSB], [http://www.ebi.ac.uk/pdbsum/5aq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5aq7 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: Large Structures]]
		+	[[Category: Synthetic construct sequences]]
	[[Category: Batyuk, A]]		[[Category: Batyuk, A]]
	[[Category: Heberling, M]]		[[Category: Heberling, M]]

OCA at 19:14, 10 May 2016

OCA — Tue, 10 May 2016 19:14:21 GMT

←Older revision		Revision as of 19:14, 10 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5aq7 is ~~ON HOLD until Paper~~ Publication	+	==DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography==
		+	<StructureSection load='5aq7' size='340' side='right' caption='[[5aq7]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5aq7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AQ7 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5aq8\|5aq8]], [[5aq9\|5aq9]], [[5aqa\|5aqa]], [[5aqb\|5aqb]]</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=5aq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aq7 OCA], [http://pdbe.org/5aq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5aq7 RCSB], [http://www.ebi.ac.uk/pdbsum/5aq7 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DARPin libraries, based on a Designed Ankyrin Repeat Protein consensus framework, are a rich source of binding partners for a wide variety of proteins. Their modular structure, stability, ease of in vitro selection and high production yields make DARPins an ideal starting point for further engineering. The X-ray structures of around 30 different DARPin complexes demonstrate their ability to facilitate crystallization of their target proteins by restricting flexibility and preventing undesired interactions of the target molecule. However, their small size (18kDa), very hydrophilic surface and repetitive structure can limit the DARPins' ability to provide essential crystal contacts and their usefulness as a search model for addressing the crystallographic phase problem in molecular replacement. To optimize DARPins for their application as crystallization chaperones, rigid domain-domain fusions of the DARPins to larger proteins, proven to yield high-resolution crystal structures, were generated. These fusions were designed in such a way that they affect only one of the terminal capping repeats of the DARPin and do not interfere with residues involved in target binding, allowing to exchange at will the binding specificities of the DARPin in the fusion construct. As a proof of principle, we designed rigid fusions of a stabilized version of Escherichia coli TEM-1 beta-lactamase to the C-terminal capping repeat of various DARPins in six different relative domain orientations. Five crystal structures representing four different fusion constructs, alone or in complex with the cognate target, show the predicted relative domain orientations and prove the validity of the concept.

-	~~Authors: Batyuk~~, A., Wu, Y., Honegger, A., Heberling, M., ~~Plueckthun, A~~.	+	DARPin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography.,Batyuk A, Wu Y, Honegger A, Heberling MM, Pluckthun A J Mol Biol. 2016 Apr 24;428(8):1574-88. doi: 10.1016/j.jmb.2016.03.002. Epub 2016, Mar 11. PMID:26975886<ref>PMID:26975886</ref>

-	~~Description: DARPin-based Crystallization Chaperones exploit Molecular Geometry as~~ a ~~Screening Dimension in Protein Crystallography~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Honegger~~, A]]	+	<div class="pdbe-citations 5aq7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Batyuk, A]]
	[[Category: Heberling, M]]		[[Category: Heberling, M]]
		+	[[Category: Honegger, A]]
	[[Category: Plueckthun, A]]		[[Category: Plueckthun, A]]
	[[Category: Wu, Y]]		[[Category: Wu, Y]]
-	[[Category: ~~Batyuk, A~~]]	+	[[Category: Chaperone]]
		+	[[Category: Crystallization chaperone]]
		+	[[Category: Rigid domain fusion]]

OCA at 09:54, 16 December 2015

OCA — Wed, 16 Dec 2015 09:54:49 GMT

←Older revision		Revision as of 09:54, 16 December 2015
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	Description: DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography		Description: DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Wu, Y]]
	[[Category: Honegger, A]]		[[Category: Honegger, A]]
	[[Category: Heberling, M]]		[[Category: Heberling, M]]
	[[Category: Plueckthun, A]]		[[Category: Plueckthun, A]]
		+	[[Category: Wu, Y]]
	[[Category: Batyuk, A]]		[[Category: Batyuk, A]]

OCA at 10:42, 7 October 2015

OCA — Wed, 07 Oct 2015 10:42:43 GMT

←Older revision		Revision as of 10:42, 7 October 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5aq7 is ON HOLD	+	The entry 5aq7 is ON HOLD until Paper Publication

	Authors: Batyuk, A., Wu, Y., Honegger, A., Heberling, M., Plueckthun, A.		Authors: Batyuk, A., Wu, Y., Honegger, A., Heberling, M., Plueckthun, A.

OCA: Protected "5aq7" [edit=sysop:move=sysop]

OCA — Wed, 30 Sep 2015 11:21:55 GMT

Protected "5aq7" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:21, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5aq7 is ON HOLD Authors: Batyuk, A., Wu, Y., Honegger, A., Heberling, M., Plueckthun, A. Description: DARPin-based Crystallization Chaperones explo...

OCA — Wed, 30 Sep 2015 11:21:54 GMT

New page: '''Unreleased structure''' The entry 5aq7 is ON HOLD Authors: Batyuk, A., Wu, Y., Honegger, A., Heberling, M., Plueckthun, A. Description: DARPin-based Crystallization Chaperones explo...

New page

'''Unreleased structure'''

The entry 5aq7 is ON HOLD

Authors: Batyuk, A., Wu, Y., Honegger, A., Heberling, M., Plueckthun, A.

Description: DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography
[[Category: Unreleased Structures]]
[[Category: Wu, Y]]
[[Category: Honegger, A]]
[[Category: Heberling, M]]
[[Category: Plueckthun, A]]
[[Category: Batyuk, A]]