6owx - Revision history

OCA at 07:18, 11 October 2023

OCA — Wed, 11 Oct 2023 07:18:32 GMT

←Older revision		Revision as of 07:18, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6owx' size='340' side='right'caption='[[6owx]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='6owx' size='340' side='right'caption='[[6owx]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6owx]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OWX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OWX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6owx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OWX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OWX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.06Å</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=6owx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6owx OCA], [~~http~~://pdbe.org/6owx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6owx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6owx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6owx ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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'>[https://proteopedia.org/fgij/fg.htm?mol=6owx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6owx OCA], [https://pdbe.org/6owx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6owx RCSB], [https://www.ebi.ac.uk/pdbsum/6owx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6owx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SPY_ECOLI SPY_ECOLI]] An ATP-independent periplasmic chaperone, decreases protein aggregation and helps protein refolding. Binds substrate over a large region of its convex inner surface (PubMed:21317898, PubMed:24497545). Substrate protein folds while it is bound to chaperone (PubMed:26619265). Increasing Spy flexibility increases its substrate affinity and overall chaperone activity (shown for 3 different substrates) (PubMed:24497545). Protects proteins in vitro against tannin inactivation; tannins have antimicrobial activity (PubMed:21317898). Overexpression enhances the stability of otherwise unstable periplasmic proteins (PubMed:21317898).<ref>PMID:21317898</ref> <ref>PMID:24497545</ref> <ref>PMID:26619265</ref>	+	[https://www.uniprot.org/uniprot/SPY_ECOLI SPY_ECOLI] An ATP-independent periplasmic chaperone, decreases protein aggregation and helps protein refolding. Binds substrate over a large region of its convex inner surface (PubMed:21317898, PubMed:24497545). Substrate protein folds while it is bound to chaperone (PubMed:26619265). Increasing Spy flexibility increases its substrate affinity and overall chaperone activity (shown for 3 different substrates) (PubMed:24497545). Protects proteins in vitro against tannin inactivation; tannins have antimicrobial activity (PubMed:21317898). Overexpression enhances the stability of otherwise unstable periplasmic proteins (PubMed:21317898).<ref>PMID:21317898</ref> <ref>PMID:24497545</ref> <ref>PMID:26619265</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Although often presented as taking single `snapshots' of the conformation of a protein, X-ray crystallography provides an averaged structure over time and space within the crystal. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes residual electron and anomalous density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data-collection and analysis strategy for partially occupied iodine anomalous signals. Using the long-wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with occupancies as low as approximately 12% is demonstrated. The number and positions of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest that the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. Finally, READ selections demonstrate that re-measured data using the new protocols are consistent with the previously characterized structural ensemble of the chaperone Spy with its client Im7. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly disordered sections of crystal structures.	+
-		+
-	Identifying dynamic, partially occupied residues using anomalous scattering.,Rocchio S, Duman R, El Omari K, Mykhaylyk V, Orr C, Yan Z, Salmon L, Wagner A, Bardwell JCA, Horowitz S Acta Crystallogr D Struct Biol. 2019 Dec 1;75(Pt 12):1084-1095. doi:, 10.1107/S2059798319014475. Epub 2019 Nov 19. PMID:31793902<ref>PMID:31793902</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6owx" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bardwell~~, J C.A~~]]	+	[[Category: Bardwell JCA]]
-	[[Category: Duman, R]]	+	[[Category: Duman R]]
-	[[Category: ~~Horowitz, S~~]]	+	[[Category: El Omari K]]
-	[[Category: ~~Mykhaylyk, V~~]]	+	[[Category: Horowitz S]]
-	[[Category: ~~Omari, K El~~]]	+	[[Category: Mykhaylyk V]]
-	[[Category: Rocchio, S]]	+	[[Category: Rocchio S]]
-	[[Category: Wagner, A]]	+	[[Category: Wagner A]]
-	[[Category: Yan, Z]]	+	[[Category: Yan Z]]
-	~~[[Category: Chaperone]]~~	+
-	~~[[Category: Periplasmic~~]]	+

OCA at 18:43, 11 December 2019

OCA — Wed, 11 Dec 2019 18:43:03 GMT

←Older revision		Revision as of 18:43, 11 December 2019
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SPY_ECOLI SPY_ECOLI]] An ATP-independent periplasmic chaperone, decreases protein aggregation and helps protein refolding. Binds substrate over a large region of its convex inner surface (PubMed:21317898, PubMed:24497545). Substrate protein folds while it is bound to chaperone (PubMed:26619265). Increasing Spy flexibility increases its substrate affinity and overall chaperone activity (shown for 3 different substrates) (PubMed:24497545). Protects proteins in vitro against tannin inactivation; tannins have antimicrobial activity (PubMed:21317898). Overexpression enhances the stability of otherwise unstable periplasmic proteins (PubMed:21317898).<ref>PMID:21317898</ref> <ref>PMID:24497545</ref> <ref>PMID:26619265</ref>		[[http://www.uniprot.org/uniprot/SPY_ECOLI SPY_ECOLI]] An ATP-independent periplasmic chaperone, decreases protein aggregation and helps protein refolding. Binds substrate over a large region of its convex inner surface (PubMed:21317898, PubMed:24497545). Substrate protein folds while it is bound to chaperone (PubMed:26619265). Increasing Spy flexibility increases its substrate affinity and overall chaperone activity (shown for 3 different substrates) (PubMed:24497545). Protects proteins in vitro against tannin inactivation; tannins have antimicrobial activity (PubMed:21317898). Overexpression enhances the stability of otherwise unstable periplasmic proteins (PubMed:21317898).<ref>PMID:21317898</ref> <ref>PMID:24497545</ref> <ref>PMID:26619265</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Although often presented as taking single `snapshots' of the conformation of a protein, X-ray crystallography provides an averaged structure over time and space within the crystal. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes residual electron and anomalous density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data-collection and analysis strategy for partially occupied iodine anomalous signals. Using the long-wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with occupancies as low as approximately 12% is demonstrated. The number and positions of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest that the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. Finally, READ selections demonstrate that re-measured data using the new protocols are consistent with the previously characterized structural ensemble of the chaperone Spy with its client Im7. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly disordered sections of crystal structures.
		+
		+	Identifying dynamic, partially occupied residues using anomalous scattering.,Rocchio S, Duman R, El Omari K, Mykhaylyk V, Orr C, Yan Z, Salmon L, Wagner A, Bardwell JCA, Horowitz S Acta Crystallogr D Struct Biol. 2019 Dec 1;75(Pt 12):1084-1095. doi:, 10.1107/S2059798319014475. Epub 2019 Nov 19. PMID:31793902<ref>PMID:31793902</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6owx" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:11, 5 June 2019

OCA — Wed, 05 Jun 2019 23:11:36 GMT

←Older revision		Revision as of 23:11, 5 June 2019
Line 3:		Line 3:
	<StructureSection load='6owx' size='340' side='right'caption='[[6owx]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='6owx' size='340' side='right'caption='[[6owx]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6owx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OWX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OWX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6owx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OWX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OWX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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=6owx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6owx OCA], [http://pdbe.org/6owx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6owx RCSB], [http://www.ebi.ac.uk/pdbsum/6owx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6owx 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=6owx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6owx OCA], [http://pdbe.org/6owx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6owx RCSB], [http://www.ebi.ac.uk/pdbsum/6owx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6owx ProSAT]</span></td></tr>
Line 13:		Line 13:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bardwell, J C.A]]		[[Category: Bardwell, J C.A]]
Line 18:		Line 19:
	[[Category: Horowitz, S]]		[[Category: Horowitz, S]]
	[[Category: Mykhaylyk, V]]		[[Category: Mykhaylyk, V]]
-	[[Category: ~~Omarib~~, K]]	+	[[Category: Omari, K El]]
	[[Category: Rocchio, S]]		[[Category: Rocchio, S]]
	[[Category: Wagner, A]]		[[Category: Wagner, A]]

OCA at 06:19, 29 May 2019

OCA — Wed, 29 May 2019 06:19:24 GMT

←Older revision		Revision as of 06:19, 29 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6owx is ~~ON HOLD~~	+	==Spy H96L:Im7 L18pI-Phe complex; multiple anomalous datasets contained herein for element identification==
-		+	<StructureSection load='6owx' size='340' side='right'caption='[[6owx]], [[Resolution\|resolution]] 2.06Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6owx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OWX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OWX FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6owx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6owx OCA], [http://pdbe.org/6owx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6owx RCSB], [http://www.ebi.ac.uk/pdbsum/6owx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6owx ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SPY_ECOLI SPY_ECOLI]] An ATP-independent periplasmic chaperone, decreases protein aggregation and helps protein refolding. Binds substrate over a large region of its convex inner surface (PubMed:21317898, PubMed:24497545). Substrate protein folds while it is bound to chaperone (PubMed:26619265). Increasing Spy flexibility increases its substrate affinity and overall chaperone activity (shown for 3 different substrates) (PubMed:24497545). Protects proteins in vitro against tannin inactivation; tannins have antimicrobial activity (PubMed:21317898). Overexpression enhances the stability of otherwise unstable periplasmic proteins (PubMed:21317898).<ref>PMID:21317898</ref> <ref>PMID:24497545</ref> <ref>PMID:26619265</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bardwell, J C.A]]
		+	[[Category: Duman, R]]
		+	[[Category: Horowitz, S]]
		+	[[Category: Mykhaylyk, V]]
		+	[[Category: Omarib, K]]
		+	[[Category: Rocchio, S]]
		+	[[Category: Wagner, A]]
		+	[[Category: Yan, Z]]
		+	[[Category: Chaperone]]
		+	[[Category: Periplasmic]]

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

OCA — Wed, 22 May 2019 04:02:38 GMT

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

←Older revision

Revision as of 04:02, 22 May 2019

OCA: New page: '''Unreleased structure''' The entry 6owx is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 May 2019 04:02:37 GMT

New page: '''Unreleased structure''' The entry 6owx is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6owx is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]