5kvw - Revision history

OCA at 10:58, 27 September 2023

2023-09-27T10:58:03Z

←Older revision		Revision as of 10:58, 27 September 2023
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	<StructureSection load='5kvw' size='340' side='right'caption='[[5kvw]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='5kvw' size='340' side='right'caption='[[5kvw]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kvw]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Katemfe Katemfe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KVW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KVW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kvw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thaumatococcus_daniellii Thaumatococcus daniellii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KVW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KVW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~>, ~~<scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 1.59Å</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]], [[5kuv\|5kuv]], [[5kuw\|5kuw]], [[5kuz\|5kuz]], [[5kv0\|5kv0]], [[5kv1\|5kv1]], [[5kv2\|5kv2]], [[5kv3\|5kv3]], [[5kv4\|5kv4]], [[5kv5\|5kv5]], [[5kv6\|5kv6]], [[5kv7\|5kv7]], [[5kvx\|5kvx]], [[5kvz\|5kvz]], [[5kw0\|5kw0]], [[5kw3\|5kw3]], [[5kw4\|5kw4]], [[5kw5\|5kw5]], [[5kw7\|5kw7]], [[5kw8\|5kw8]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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=5kvw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kvw OCA], [~~http~~://pdbe.org/5kvw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kvw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kvw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kvw 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=5kvw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kvw OCA], [https://pdbe.org/5kvw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kvw RCSB], [https://www.ebi.ac.uk/pdbsum/5kvw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kvw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/THM1_THADA THM1_THADA]] Taste-modifying protein; intensely sweet-tasting. It is 100000 times sweeter than sucrose on a molar basis.	+	[https://www.uniprot.org/uniprot/THM1_THADA THM1_THADA] Taste-modifying protein; intensely sweet-tasting. It is 100000 times sweeter than sucrose on a molar basis.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Katemfe]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bedem, H van den~~]]	+	[[Category: Thaumatococcus daniellii]]
-	[[Category: Fraser~~, J S~~]]	+	[[Category: Fraser JS]]
-	[[Category: Gonzalez, A]]	+	[[Category: Gonzalez A]]
-	[[Category: Keedy~~, D A~~]]	+	[[Category: Keedy DA]]
-	[[Category: Kenner~~, L R~~]]	+	[[Category: Kenner LR]]
-	[[Category: Russi, S]]	+	[[Category: Russi S]]
-	[[Category: ~~Conformational variation]]~~	+	[[Category: Van den Bedem H]]
-	~~[[Category: Plant protein]]~~	+
-	~~[[Category: Radiation damage~~]]	+

OCA at 07:47, 27 November 2019

2019-11-27T07:47:32Z

←Older revision		Revision as of 07:47, 27 November 2019
Line 1:		Line 1:

	==T. danielli thaumatin at 100K, Data set 1==		==T. danielli thaumatin at 100K, Data set 1==
-	<StructureSection load='5kvw' size='340' side='right' caption='[[5kvw]], [[Resolution\|resolution]] 1.59Å' scene=''>	+	<StructureSection load='5kvw' size='340' side='right'caption='[[5kvw]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kvw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KVW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KVW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kvw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Katemfe Katemfe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KVW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KVW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></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]], [[5kuv\|5kuv]], [[5kuw\|5kuw]], [[5kuz\|5kuz]], [[5kv0\|5kv0]], [[5kv1\|5kv1]], [[5kv2\|5kv2]], [[5kv3\|5kv3]], [[5kv4\|5kv4]], [[5kv5\|5kv5]], [[5kv6\|5kv6]], [[5kv7\|5kv7]], [[5kvx\|5kvx]], [[5kvz\|5kvz]], [[5kw0\|5kw0]], [[5kw3\|5kw3]], [[5kw4\|5kw4]], [[5kw5\|5kw5]], [[5kw7\|5kw7]], [[5kw8\|5kw8]]</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]], [[5kuv\|5kuv]], [[5kuw\|5kuw]], [[5kuz\|5kuz]], [[5kv0\|5kv0]], [[5kv1\|5kv1]], [[5kv2\|5kv2]], [[5kv3\|5kv3]], [[5kv4\|5kv4]], [[5kv5\|5kv5]], [[5kv6\|5kv6]], [[5kv7\|5kv7]], [[5kvx\|5kvx]], [[5kvz\|5kvz]], [[5kw0\|5kw0]], [[5kw3\|5kw3]], [[5kw4\|5kw4]], [[5kw5\|5kw5]], [[5kw7\|5kw7]], [[5kw8\|5kw8]]</td></tr>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Katemfe]]
		+	[[Category: Large Structures]]
	[[Category: Bedem, H van den]]		[[Category: Bedem, H van den]]
	[[Category: Fraser, J S]]		[[Category: Fraser, J S]]

OCA at 08:19, 18 January 2017

2017-01-18T08:19:46Z

←Older revision		Revision as of 08:19, 18 January 2017
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/THM1_THADA THM1_THADA]] Taste-modifying protein; intensely sweet-tasting. It is 100000 times sweeter than sucrose on a molar basis.		[[http://www.uniprot.org/uniprot/THM1_THADA THM1_THADA]] Taste-modifying protein; intensely sweet-tasting. It is 100000 times sweeter than sucrose on a molar basis.
		+	<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 5kvw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:13, 10 September 2016

2016-09-10T21:13:21Z

←Older revision		Revision as of 21:13, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kvw is ~~ON HOLD~~	+	==T. danielli thaumatin at 100K, Data set 1==
-		+	<StructureSection load='5kvw' size='340' side='right' caption='[[5kvw]], [[Resolution\|resolution]] 1.59Å' 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'>[[5kvw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KVW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KVW FirstGlance]. <br>
-	~~Description~~: T. ~~danielli thaumatin at 100K, Data set 1~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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]], [[5kuv\|5kuv]], [[5kuw\|5kuw]], [[5kuz\|5kuz]], [[5kv0\|5kv0]], [[5kv1\|5kv1]], [[5kv2\|5kv2]], [[5kv3\|5kv3]], [[5kv4\|5kv4]], [[5kv5\|5kv5]], [[5kv6\|5kv6]], [[5kv7\|5kv7]], [[5kvx\|5kvx]], [[5kvz\|5kvz]], [[5kw0\|5kw0]], [[5kw3\|5kw3]], [[5kw4\|5kw4]], [[5kw5\|5kw5]], [[5kw7\|5kw7]], [[5kw8\|5kw8]]</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=5kvw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kvw OCA], [http://pdbe.org/5kvw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kvw RCSB], [http://www.ebi.ac.uk/pdbsum/5kvw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kvw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/THM1_THADA THM1_THADA]] Taste-modifying protein; intensely sweet-tasting. It is 100000 times sweeter than sucrose on a molar basis.
		+	__TOC__
		+	</StructureSection>
		+	[[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: Plant protein]]
-	[[Category: ~~Keedy, D.A~~]]	+	[[Category: Radiation damage]]

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

2016-07-27T13:25:36Z

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

←Older revision

Revision as of 13:25, 27 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kvw is ON HOLD Authors: Russi, S., Gonzalez, A., Kenner, L.R., Keedy, D.A., Fraser, J.S., van den Bedem, H. Description: T. danielli thaumatin at ...

2016-07-27T13:25:35Z

New page: '''Unreleased structure''' The entry 5kvw is ON HOLD Authors: Russi, S., Gonzalez, A., Kenner, L.R., Keedy, D.A., Fraser, J.S., van den Bedem, H. Description: T. danielli thaumatin at ...

New page

'''Unreleased structure'''

The entry 5kvw is ON HOLD

Authors: Russi, S., Gonzalez, A., Kenner, L.R., Keedy, D.A., Fraser, J.S., van den Bedem, H.

Description: T. danielli thaumatin at 100K, Data set 1
[[Category: Unreleased Structures]]
[[Category: Van Den Bedem, H]]
[[Category: Gonzalez, A]]
[[Category: Russi, S]]
[[Category: Fraser, J.S]]
[[Category: Kenner, L.R]]
[[Category: Keedy, D.A]]