5D57

In meso X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K

Summary for 5D57

• Entry DOI: 10.2210/pdb5d57/pdb
• Descriptor: Diacylglycerol kinase, (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE (3 entities in total)
• Functional Keywords: transferase
• Biological source: Escherichia coli K-12
• Cellular location: Cell inner membrane; Multi-pass membrane protein: P0ABN1
• Total number of polymer chains: 6
• Total formula weight: 90258.07

Authors

Huang, C.-Y.,Howe, N.,Olieric, V.,Wang, M.,Caffrey, M. (deposition date: 2015-08-10, release date: 2016-01-13, Last modification date: 2024-01-10)

Primary citation

Huang, C.Y.,Olieric, V.,Ma, P.,Howe, N.,Vogeley, L.,Liu, X.,Warshamanage, R.,Weinert, T.,Panepucci, E.,Kobilka, B.,Diederichs, K.,Wang, M.,Caffrey, M.
In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures.
Acta Crystallogr D Struct Biol, 72:93-112, 2016

PubMed Abstract: 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, α-helical and β-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.

PubMed: 26894538
DOI: 10.1107/S2059798315021683

Experimental method

X-RAY DIFFRACTION (2.8 Å)