5d56: Difference between revisions
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==In meso in situ serial X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K== | ==In meso in situ serial X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K== | ||
<StructureSection load='5d56' size='340' side='right' caption='[[5d56]], [[Resolution|resolution]] 2.80Å' scene=''> | <StructureSection load='5d56' size='340' side='right'caption='[[5d56]], [[Resolution|resolution]] 2.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5d56]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D56 FirstGlance]. <br> | <table><tr><td colspan='2'>[[5d56]] 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=5D56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D56 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>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</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=78M:(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5d56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d56 OCA], [http://pdbe.org/5d56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d56 RCSB], [http://www.ebi.ac.uk/pdbsum/5d56 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=5d56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d56 OCA], [http://pdbe.org/5d56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d56 RCSB], [http://www.ebi.ac.uk/pdbsum/5d56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d56 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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</div> | </div> | ||
<div class="pdbe-citations 5d56" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5d56" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Diacylglycerol kinase 3D structures|Diacylglycerol kinase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Diacylglycerol kinase]] | [[Category: Diacylglycerol kinase]] | ||
[[Category: Ecoli]] | |||
[[Category: Large Structures]] | |||
[[Category: Caffrey, M]] | [[Category: Caffrey, M]] | ||
[[Category: Diederichs, K]] | [[Category: Diederichs, K]] | ||
Revision as of 13:37, 1 April 2020
In meso in situ serial X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 KIn meso in situ serial X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K
Structural highlights
Function[KDGL_ECOLI] Recycling of diacylglycerol produced during the turnover of membrane phospholipid. Publication Abstract from PubMedHere, 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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