I have seen similar density with a fatty acid (C16 or C18). In our case
the there was also a lysine side chain forming a salt bridge with the
carboxylate. Furthermore, the pocket was very hydrophobic. What about
this one?
-Peer
On 02.04.2019 03:12, Zhen Luo wrote:
Hi everyone,
Thank you very much for your help and time. A PEG fragment indeed
seems to fit into the density. Thanks again!
Best regards,
Zhen
*From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Zhen
Luo <z....@imb.uq.edu.au>
*Reply-To: *Zhen Luo <z....@imb.uq.edu.au>
*Date: *Tuesday, 2 April 2019 at 9:01 AM
*To: *"CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK>
*Subject: *[ccp4bb] unidentified crescent-shaped electron density
Dear all,
Could you please shed some light on what this crescent-shaped density
around the lysine side chain might belong to? I now have two unrelated
protein structures where this kind of density can be found surrounding
a lysine side chain.
Protein 1cid:image009.png@01D4E932.5B911B60
Protein 2cid:image012.png@01D4E932.5B911B60
2FOFC maps were contoured at around 1.5 sigma, FOFC map at 3 sigma.
One protein was crystallised in 0.1 M CaCl_2 and 20% PEG 3350; the
other in 10% PEG 20000, 20% PEG MME 550, 0.03 M CaCl_2 /MgCl_2 , 0.1 M
MES/imidazole. Protein buffers contained 0.025 M HEPES and 0.15 M
NaCl. None of these fitted in well. Could it be cleaved PEG?
Any suggestion would be greatly appreciated. Thanks in advance!
Best regards,
Zhen Luo
School of Chemistry and Molecular Biosciences
The University of Queensland, Australia
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****************************
Peer Mittl, PD Dr.
Biochemisches Institut
Universität Zürich
Room 44M03
Winterthurer Strasse 190
CH-8057 Zürich
Tel. +41-(0)44-6356559
Mobile +41-(0)76-2776566
Fax. +41-(0)44-6356805
Mail mi...@bioc.uzh.ch
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