Dear Sudhir,
A blob surrounded by three Asp residues looks like a positively charged ion.
What else (buffer, additives) is in your crystallization drop? I would also try
to fit cysteine/serine. At 2 Å you will quickly see whether or not this is
correct.
Good luck!
Herman
________________________________
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Sudhir Kumar
Sent: Friday, February 10, 2012 7:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unidentified density
Dear all,
I have a 2 A structure of an enzyme which show 12 molecules per
asymmetric unit. While placing waters i found out some blobs where i could not
model any ligand. It is surrounded by 3 Asp molecules. I have attached
screenshot of the blob at 1.5 sigma cutoff 2fo-fc density. Crystallization
condition had following precipitants: PEG 1000, Peg 3350, MPD, Ethylene
glycol,and protein contained Glycerol. My protein is known to bind
Cysteine/Serine, though i haven't added any in crystallization buffer. any
suggestion what it might be are welcome. thanks in advance
--
best regards
Sudhir Kumar
Research Scholar
C/O Dr. S. Gourinath
Structural Biology Laboratory
SLS, JNU,
New Delhi-110067
