"The protein was neither crystallized nor purified with any substrate"
On returning to an old project, I discovered that a site believed to be empty
was actually at around 25% occupancy in the crystal structure, with the native
ligand. Since the ligand was not added to the crystallization mix, that means
it was pulled through the purification procedure from the expression system.
Modern purification procedures are much shorter and quicker than in the old
days. Ammonium sulfate cuts, multiple ion exchange columns and extensive
dialysis have been replaced by affinity columns. And if you are replacing
extensive dialysis with centrifugal filters, you shouldn't be surprised if it
isn't as effective.
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All Things Serve the Beam
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
[email protected]
________________________________
From: CCP4 bulletin board <[email protected]> on behalf of Manjula Ramu
<[email protected]>
Sent: Tuesday, March 25, 2025 16:07
To: [email protected] <[email protected]>
Subject: [ccp4bb] Unexplained electron density
Dear All,
I have a trimeric protein structure with unexplained electron density in the
catalytic pocket. The protein was neither crystallized nor purified with any
substrate, and the buffer and crystallization conditions contained only Tris,
NaCl, ammonium sulfate, and 3% 2-propanol.
I have attached the images of the electron density and would appreciate any
insights on identifying this unknown feature.
----------------------------------------------------
Thanks and Regards,
Manjula
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