5kuv - Revision history

OCA at 10:55, 27 September 2023

OCA — Wed, 27 Sep 2023 10:55:42 GMT

←Older revision		Revision as of 10:55, 27 September 2023
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	<StructureSection load='5kuv' size='340' side='right'caption='[[5kuv]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5kuv' size='340' side='right'caption='[[5kuv]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kuv]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KUV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KUV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kuv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KUV FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[5kul\|5kul]], [[5kun\|5kun]], [[5kuo\|5kuo]], [[5kuq\|5kuq]], [[5kur\|5kur]], [[5kus\|5kus]], [[5kuu\|5kuu]], [[5kuw\|5kuw]], [[5kuz\|5kuz]], [[5kv0\|5kv0]], [[5kv1\|5kv1]], [[5kv2\|5kv2]], [[5kv3\|5kv3]], [[5kv4\|5kv4]], [[5kv5\|5kv5]], [[5kv6\|5kv6]], [[5kv7\|5kv7]]</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]] 1.7Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">PPIA, CYPA ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN])</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=5kuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kuv OCA], [https://pdbe.org/5kuv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kuv RCSB], [https://www.ebi.ac.uk/pdbsum/5kuv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kuv ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </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=5kuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kuv OCA], [~~http~~://pdbe.org/5kuv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kuv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kuv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kuv ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PPIA_HUMAN PPIA_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.	+	[https://www.uniprot.org/uniprot/PPIA_HUMAN PPIA_HUMAN] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Peptidylprolyl isomerase]]~~	+	[[Category: Fraser JS]]
-	~~[[Category: Bedem, H van den]]~~	+	[[Category: Gonzalez A]]
-	[[Category: Fraser~~, J S~~]]	+	[[Category: Keedy DA]]
-	[[Category: Gonzalez, A]]	+	[[Category: Kenner LR]]
-	[[Category: Keedy~~, D A~~]]	+	[[Category: Russi S]]
-	[[Category: Kenner~~, L R~~]]	+	[[Category: Van den Bedem H]]
-	[[Category: Russi, S]]	+
-	[[Category: ~~Conformational variation]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Radiation damage~~]]	+

OCA at 07:46, 27 November 2019

OCA — Wed, 27 Nov 2019 07:46:35 GMT

←Older revision		Revision as of 07:46, 27 November 2019
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	==Human cyclophilin A at 100K, Data set 8==		==Human cyclophilin A at 100K, Data set 8==
-	<StructureSection load='5kuv' size='340' side='right' caption='[[5kuv]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5kuv' size='340' side='right'caption='[[5kuv]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5kuv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KUV FirstGlance]. <br>		<table><tr><td colspan='2'>[[5kuv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KUV FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5kuv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5kuv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cyclophilin 3D structures\|Cyclophilin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Peptidylprolyl isomerase]]		[[Category: Peptidylprolyl isomerase]]
	[[Category: Bedem, H van den]]		[[Category: Bedem, H van den]]

OCA at 13:03, 6 November 2017

OCA — Mon, 06 Nov 2017 13:03:56 GMT

←Older revision		Revision as of 13:03, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5kuv' size='340' side='right' caption='[[5kuv]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5kuv' size='340' side='right' caption='[[5kuv]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kuv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KUV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kuv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KUV FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kul\|5kul]], [[5kun\|5kun]], [[5kuo\|5kuo]], [[5kuq\|5kuq]], [[5kur\|5kur]], [[5kus\|5kus]], [[5kuu\|5kuu]], [[5kuw\|5kuw]], [[5kuz\|5kuz]], [[5kv0\|5kv0]], [[5kv1\|5kv1]], [[5kv2\|5kv2]], [[5kv3\|5kv3]], [[5kv4\|5kv4]], [[5kv5\|5kv5]], [[5kv6\|5kv6]], [[5kv7\|5kv7]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kul\|5kul]], [[5kun\|5kun]], [[5kuo\|5kuo]], [[5kuq\|5kuq]], [[5kur\|5kur]], [[5kus\|5kus]], [[5kuu\|5kuu]], [[5kuw\|5kuw]], [[5kuz\|5kuz]], [[5kv0\|5kv0]], [[5kv1\|5kv1]], [[5kv2\|5kv2]], [[5kv3\|5kv3]], [[5kv4\|5kv4]], [[5kv5\|5kv5]], [[5kv6\|5kv6]], [[5kv7\|5kv7]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIA, CYPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </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=5kuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kuv OCA], [http://pdbe.org/5kuv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kuv RCSB], [http://www.ebi.ac.uk/pdbsum/5kuv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kuv 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=5kuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kuv OCA], [http://pdbe.org/5kuv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kuv RCSB], [http://www.ebi.ac.uk/pdbsum/5kuv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kuv ProSAT]</span></td></tr>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Peptidylprolyl isomerase]]		[[Category: Peptidylprolyl isomerase]]
	[[Category: Bedem, H van den]]		[[Category: Bedem, H van den]]

OCA at 09:47, 4 January 2017

OCA — Wed, 04 Jan 2017 09:47:07 GMT

←Older revision		Revision as of 09:47, 4 January 2017
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PPIA_HUMAN PPIA_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.		[[http://www.uniprot.org/uniprot/PPIA_HUMAN PPIA_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein crystallography data collection at synchrotrons is routinely carried out at cryogenic temperatures to mitigate radiation damage. Although damage still takes place at 100 K and below, the immobilization of free radicals increases the lifetime of the crystals by approximately 100-fold. Recent studies have shown that flash-cooling decreases the heterogeneity of the conformational ensemble and can hide important functional mechanisms from observation. These discoveries have motivated increasing numbers of experiments to be carried out at room temperature. However, the trade-offs between increased risk of radiation damage and increased observation of alternative conformations at room temperature relative to cryogenic temperature have not been examined. A considerable amount of effort has previously been spent studying radiation damage at cryo-temperatures, but the relevance of these studies to room temperature diffraction is not well understood. Here, the effects of radiation damage on the conformational landscapes of three different proteins (T. danielli thaumatin, hen egg-white lysozyme and human cyclophilin A) at room (278 K) and cryogenic (100 K) temperatures are investigated. Increasingly damaged datasets were collected at each temperature, up to a maximum dose of the order of 107 Gy at 100 K and 105 Gy at 278 K. Although it was not possible to discern a clear trend between damage and multiple conformations at either temperature, it was observed that disorder, monitored by B-factor-dependent crystallographic order parameters, increased with higher absorbed dose for the three proteins at 100 K. At 278 K, however, the total increase in this disorder was only statistically significant for thaumatin. A correlation between specific radiation damage affecting side chains and the amount of disorder was not observed. This analysis suggests that elevated conformational heterogeneity in crystal structures at room temperature is observed despite radiation damage, and not as a result thereof.
		+
		+	Conformational variation of proteins at room temperature is not dominated by radiation damage.,Russi S, Gonzalez A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H J Synchrotron Radiat. 2017 Jan 1;24(Pt 1):73-82. doi: 10.1107/S1600577516017343. , Epub 2017 Jan 1. PMID:28009548<ref>PMID:28009548</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5kuv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:29, 10 August 2016

OCA — Wed, 10 Aug 2016 16:29:51 GMT

←Older revision		Revision as of 16:29, 10 August 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kuv ~~is ON HOLD~~	+	==Human cyclophilin A at 100K, Data set 8==
-		+	<StructureSection load='5kuv' size='340' side='right' caption='[[5kuv]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors~~: ~~Russi, S~~., ~~Gonzalez~~, A., ~~Kenner~~, L.R., ~~Keedy~~, D.A., ~~Fraser~~, J.S., ~~van den Bedem~~, H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5kuv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KUV FirstGlance]. <br>
-	~~Description~~: ~~Human cyclophilin A at 100K, Data set 8~~	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kul\|5kul]], [[5kun\|5kun]], [[5kuo\|5kuo]], [[5kuq\|5kuq]], [[5kur\|5kur]], [[5kus\|5kus]], [[5kuu\|5kuu]], [[5kuw\|5kuw]], [[5kuz\|5kuz]], [[5kv0\|5kv0]], [[5kv1\|5kv1]], [[5kv2\|5kv2]], [[5kv3\|5kv3]], [[5kv4\|5kv4]], [[5kv5\|5kv5]], [[5kv6\|5kv6]], [[5kv7\|5kv7]]</td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>
-	[[Category: ~~Van Den~~ Bedem, H]]	+	<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=5kuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kuv OCA], [http://pdbe.org/5kuv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kuv RCSB], [http://www.ebi.ac.uk/pdbsum/5kuv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kuv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PPIA_HUMAN PPIA_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Peptidylprolyl isomerase]]
		+	[[Category: Bedem, H van den]]
		+	[[Category: Fraser, J S]]
	[[Category: Gonzalez, A]]		[[Category: Gonzalez, A]]
		+	[[Category: Keedy, D A]]
		+	[[Category: Kenner, L R]]
	[[Category: Russi, S]]		[[Category: Russi, S]]
-	[[Category: ~~Fraser, J.S~~]]	+	[[Category: Conformational variation]]
-	[[Category: ~~Kenner, L.R~~]]	+	[[Category: Isomerase]]
-	[[Category: ~~Keedy, D.A~~]]	+	[[Category: Radiation damage]]

OCA at 13:23, 27 July 2016

OCA — Wed, 27 Jul 2016 13:23:22 GMT

←Older revision		Revision as of 13:23, 27 July 2016
Line 3:		Line 3:
	The entry 5kuv is ON HOLD		The entry 5kuv is ON HOLD

-	Authors: ~~Silvia~~ Russi, ~~Ana~~ Gonzalez, ~~Lillian R~~. Kenner, ~~Daniel A~~. Keedy, ~~James S~~. Fraser, ~~Henry~~ van den Bedem	+	Authors: Russi, S., Gonzalez, A., Kenner, L.R., Keedy, D.A., Fraser, J.S., van den Bedem, H.

-	Description: Human cyclophilin A @ 100K, Data set #8	+	Description: Human cyclophilin A at 100K, Data set 8
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Silvia Russi~~, ~~Ana~~ Gonzalez, ~~Lillian R~~. Kenner, ~~Daniel A~~. Keedy, ~~James S~~. ~~Fraser, Henry Van Den Bedem~~]]	+	[[Category: Van Den Bedem, H]]
		+	[[Category: Gonzalez, A]]
		+	[[Category: Russi, S]]
		+	[[Category: Fraser, J.S]]
		+	[[Category: Kenner, L.R]]
		+	[[Category: Keedy, D.A]]

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

OCA — Tue, 26 Jul 2016 12:58:09 GMT

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

←Older revision

Revision as of 12:58, 26 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kuv is ON HOLD Authors: Silvia Russi, Ana Gonzalez, Lillian R. Kenner, Daniel A. Keedy, James S. Fraser, Henry van den Bedem Description: Human cy...

OCA — Tue, 26 Jul 2016 12:58:08 GMT

New page: '''Unreleased structure''' The entry 5kuv is ON HOLD Authors: Silvia Russi, Ana Gonzalez, Lillian R. Kenner, Daniel A. Keedy, James S. Fraser, Henry van den Bedem Description: Human cy...

New page

'''Unreleased structure'''

The entry 5kuv is ON HOLD

Authors: Silvia Russi, Ana Gonzalez, Lillian R. Kenner, Daniel A. Keedy, James S. Fraser, Henry van den Bedem

Description: Human cyclophilin A @ 100K, Data set #8
[[Category: Unreleased Structures]]
[[Category: Silvia Russi, Ana Gonzalez, Lillian R. Kenner, Daniel A. Keedy, James S. Fraser, Henry Van Den Bedem]]