Dear Mengxia,
the lower part could well be a sulfate ion. For the upper part, it is
difficult to guess from a static picture. Unfortunately, at the
resolution you have there are no programs which can build an unknown
small molecule from scratch according to the density. You have to guess,
fit it and refine and look if it's ok. I would also check whether a
natural ligand of the protein (substrate, product, effector molecule)
would fit. They sometimes remain attached during the whole purification
procedure. A trick to get an idea where heavy atoms like sulfur are
located is to scroll the contour level up. If the density for e.g. the
center disappears very late, when most of the other density is no longer
visible, it must be a sulfur or other heavy atom.
Good luck!
Herman
________________________________
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
Behalf Of mengxiao lv
Sent: Tuesday, February 10, 2009 6:24 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] unknown density for a small molecule
Dear All,
When I was refining my structure, I found some unmodeled blobs,
shown as attached images (contoured at 3 sigma for Fo-Fc, Rfree 0.21 and
Rfactor 0.18, refined to 1.9 angstrom ).
The protein was expressed in E.coli and purified by nickel
column and gel filtration, both in tris buffer. The crystallization
condition has 2 M ammonium sulfate and 0.1 M sodium acetate.
The lower part looks like a sulfate group, which is held by one
Arg, one his, one lys and one asn. The latter three residues are from
another asymmetric unit.
The other end of the small molecule is stunk by the rings of Tyr
and Phe. It also interacts with the OH group of another tyr and one
water molecule.
Is there a program can build small molecule models according to
the densities? Or could anyone tell what it might be from the density?
Thanks a lot! Any suggestions will be appreciated!
Mengxiao
