5d57 - Revision history

OCA at 11:24, 10 January 2024

OCA — Wed, 10 Jan 2024 11:24:30 GMT

←Older revision		Revision as of 11:24, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5d57]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D57 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5d57]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D57 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=78M:(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</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]] 2.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=78M:(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</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=5d57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d57 OCA], [https://pdbe.org/5d57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d57 RCSB], [https://www.ebi.ac.uk/pdbsum/5d57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d57 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=5d57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d57 OCA], [https://pdbe.org/5d57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d57 RCSB], [https://www.ebi.ac.uk/pdbsum/5d57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d57 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:22, 21 June 2023

OCA — Wed, 21 Jun 2023 10:22:21 GMT

←Older revision		Revision as of 10:22, 21 June 2023
Line 3:		Line 3:
	<StructureSection load='5d57' size='340' side='right'caption='[[5d57]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5d57' size='340' side='right'caption='[[5d57]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d57]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D57 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5D57 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d57]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D57 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=78M:(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=78M:(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dgkA, b4042, JW4002 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5d57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d57 OCA], [https://pdbe.org/5d57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d57 RCSB], [https://www.ebi.ac.uk/pdbsum/5d57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d57 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/Diacylglycerol_kinase Diacylglycerol kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.107 2.7.1.107] </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=5d57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d57 OCA], [~~http~~://pdbe.org/5d57 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5d57 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5d57 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5d57 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KDGL_ECOLI KDGL_ECOLI]] Recycling of diacylglycerol produced during the turnover of membrane phospholipid.	+	[https://www.uniprot.org/uniprot/KDGL_ECOLI KDGL_ECOLI] Recycling of diacylglycerol produced during the turnover of membrane phospholipid.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Diacylglycerol kinase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Caffrey, M]]	+	[[Category: Caffrey M]]
-	[[Category: Howe, N]]	+	[[Category: Howe N]]
-	[[Category: Huang, C Y]]	+	[[Category: Huang C-Y]]
-	[[Category: Olieric, V]]	+	[[Category: Olieric V]]
-	[[Category: Wang, M]]	+	[[Category: Wang M]]
-	~~[[Category: Transferase~~]]	+

OCA at 10:37, 1 April 2020

OCA — Wed, 01 Apr 2020 10:37:56 GMT

←Older revision		Revision as of 10:37, 1 April 2020
Line 1:		Line 1:

	==In meso X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K==		==In meso X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K==
-	<StructureSection load='5d57' size='340' side='right' caption='[[5d57]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5d57' size='340' side='right'caption='[[5d57]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d57]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D57 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D57 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d57]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D57 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D57 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=78M:(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=78M:(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dgkA, b4042, JW4002 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diacylglycerol_kinase Diacylglycerol kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.107 2.7.1.107] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diacylglycerol_kinase Diacylglycerol kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.107 2.7.1.107] </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=5d57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d57 OCA], [http://pdbe.org/5d57 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d57 RCSB], [http://www.ebi.ac.uk/pdbsum/5d57 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=5d57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d57 OCA], [http://pdbe.org/5d57 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d57 RCSB], [http://www.ebi.ac.uk/pdbsum/5d57 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d57 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5d57" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5d57" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Diacylglycerol kinase 3D structures\|Diacylglycerol kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Diacylglycerol kinase]]		[[Category: Diacylglycerol kinase]]
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Caffrey, M]]		[[Category: Caffrey, M]]
	[[Category: Howe, N]]		[[Category: Howe, N]]

OCA at 07:06, 2 March 2016

OCA — Wed, 02 Mar 2016 07:06:45 GMT

←Older revision		Revision as of 07:06, 2 March 2016
Line 1:		Line 1:
		+
	==In meso X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K==		==In meso X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K==
	<StructureSection load='5d57' size='340' side='right' caption='[[5d57]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5d57' size='340' side='right' caption='[[5d57]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 9:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/KDGL_ECOLI KDGL_ECOLI]] Recycling of diacylglycerol produced during the turnover of membrane phospholipid.		[[http://www.uniprot.org/uniprot/KDGL_ECOLI KDGL_ECOLI]] Recycling of diacylglycerol produced during the turnover of membrane phospholipid.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Here, a method for presenting crystals of soluble and membrane proteins growing in the lipid cubic or sponge phase for in situ diffraction data collection at cryogenic temperatures is introduced. The method dispenses with the need for the technically demanding and inefficient crystal-harvesting step that is an integral part of the lipid cubic phase or in meso method of growing crystals. Crystals are dispersed in a bolus of mesophase sandwiched between thin plastic windows. The bolus contains tens to hundreds of crystals, visible with an in-line microscope at macromolecular crystallography synchrotron beamlines and suitably disposed for conventional or serial crystallographic data collection. Wells containing the crystal-laden boluses are removed individually from hermetically sealed glass plates in which crystallization occurs, affixed to pins on goniometer bases and excess precipitant is removed from around the mesophase. The wells are snap-cooled in liquid nitrogen, stored and shipped in Dewars, and manually or robotically mounted on a goniometer in a cryostream for diffraction data collection at 100 K, as is performed routinely with standard, loop-harvested crystals. The method is a variant on the recently introduced in meso in situ serial crystallography (IMISX) method that enables crystallographic measurements at cryogenic temperatures where crystal lifetimes are enormously enhanced whilst reducing protein consumption dramatically. The new approach has been used to generate high-resolution crystal structures of a G-protein-coupled receptor, alpha-helical and beta-barrel transporters and an enzyme as model integral membrane proteins. Insulin and lysozyme were used as test soluble proteins. The quality of the data that can be generated by this method was attested to by performing sulfur and bromine SAD phasing with two of the test proteins.
		+
		+	In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures.,Huang CY, Olieric V, Ma P, Howe N, Vogeley L, Liu X, Warshamanage R, Weinert T, Panepucci E, Kobilka B, Diederichs K, Wang M, Caffrey M Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):93-112. doi:, 10.1107/S2059798315021683. Epub 2016 Jan 1. PMID:26894538<ref>PMID:26894538</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5d57" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 20:30, 13 January 2016

OCA — Wed, 13 Jan 2016 20:30:50 GMT

←Older revision		Revision as of 20:30, 13 January 2016
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==In meso X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K==
-		+	<StructureSection load='5d57' size='340' side='right' caption='[[5d57]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~The entry~~ 5d57 is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5d57]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D57 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D57 FirstGlance]. <br>
-	~~Authors~~: ~~Huang~~, C.-Y.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=78M:(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</scene></td></tr>
-		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diacylglycerol_kinase Diacylglycerol kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.107 2.7.1.107] </span></td></tr>
-	~~Description~~:	+	<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=5d57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d57 OCA], [http://pdbe.org/5d57 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d57 RCSB], [http://www.ebi.ac.uk/pdbsum/5d57 PDBsum]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: Huang, C.-Y]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KDGL_ECOLI KDGL_ECOLI]] Recycling of diacylglycerol produced during the turnover of membrane phospholipid.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Diacylglycerol kinase]]
		+	[[Category: Caffrey, M]]
		+	[[Category: Howe, N]]
		+	[[Category: Huang, C Y]]
		+	[[Category: Olieric, V]]
		+	[[Category: Wang, M]]
		+	[[Category: Transferase]]

OCA: Protected "5d57" [edit=sysop:move=sysop]

OCA — Thu, 20 Aug 2015 11:23:10 GMT

Protected "5d57" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:23, 20 August 2015

OCA: New page: '''Unreleased structure''' The entry 5d57 is ON HOLD until Paper Publication Authors: Huang, C.-Y. Description: Category: Unreleased Structures Category: Huang, C.-Y

OCA — Thu, 20 Aug 2015 11:23:09 GMT

New page: '''Unreleased structure''' The entry 5d57 is ON HOLD until Paper Publication Authors: Huang, C.-Y. Description: Category: Unreleased Structures Category: Huang, C.-Y

New page

'''Unreleased structure'''

The entry 5d57 is ON HOLD until Paper Publication

Authors: Huang, C.-Y.

Description:
[[Category: Unreleased Structures]]
[[Category: Huang, C.-Y]]