Hi Mengxiao,
The density sure reminds me of a nucleotide.
Note the pi-pi stacking of the planar part
between Tyr and Phe, and in the third stereo
picture you attached, projections at what could
be the 2 and 6 positions remind me of Guanine...
plus there are Arg, Lys, etc. pointing toward
where there could be a phosphate group. Even if
the density is not quite 'big enough' to fit it,
I'd give it a try.
In addition to components of your
crystallization conditions, you might consider
that something was either co-purified with your
protein, or is contaminating your reagents.
Good luck!
-pamela
At 11:37 AM -0500 2/10/09, mengxiao lv wrote:
Thank you so much for the replies!
I should clarify in my mail that the two images
are actually from one blob, just viewed from two
sides. Sorry for the confusing. I enclosed some
stereo densities for the same blob in this mail.
As Artem said, it is very similar to isopentenyl
phosphate. The upper part is planar. I agree
with Marc and Eleanor's suggestion that the
molecule is from the crystallization solution. I
have tried to model one acetate into the
density, and it fits well. And the lower part
can also model into a sulfate. However, I will
see the positive density for the missed link
between acetate and sulfate. THe pH for
crystallization is 4.6. Will acetate form some
compound with sulfate?
To Jan and Rajesh, I didn't use MES buffer in
the whole procedures. Also, the ring in MES
might be too large for the upper part.
I also get suggestions to model a molecule with
a sugar ring, from Kornelius, Poul, Daniele. The
images I attached are not clear, and I don't
think the density is large enough for a five or
six member ring.
Thanks again for the help! Hope the new images
will make things clear. I appreciate any
suggestions!
Mengxiao
On Tue, Feb 10, 2009 at 2:08 AM, Kontopidis
George
<<mailto:gkontopi...@vet.uth.gr>gkontopi...@vet.uth.gr>
wrote:
Dear Mengxiao,
From my experience I would say that the two e.
densities (blob1 and blob2) are present the same
molecule.
What that might be is more difficult to answer.
Based in the concentration you gave us and the
electron density volume I would say that is more
likely to be ammonium sulphate (NH4 and SO4).
As you say the lower part looks like SO4 and
make sense to interact with Arg, Lys and Asn and
the other end looks like NH4.
But those two group there and give it one round
of refinement. Check the B factors at the end
Do they make sense (directions of H-bonds,
distance between NH4 and SO4)? Is the Bfactor
similar for NH4 and SO4
They should not have a difference greater than 50%.
You could try also Na in stead of NH4
George
From: CCP4 bulletin board
[mailto:<mailto:CCP4BB@JISCMAIL.AC.UK>ccp...@jiscmail.ac.uk]
On Behalf Of mengxiao lv
Sent: Tuesday, February 10, 2009 7:24 AM
To: <mailto:CCP4BB@JISCMAIL.AC.UK>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
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--
----
Pamela J. Focia, Ph.D.
Research Assistant Professor
Structural Biology Facility Manager
Robert H. Lurie Comprehensive Cancer Center
in the Departments of:
Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine,
and Biochemistry, Molecular Biology & Cell Biology,
Northwestern University
303 E. Chicago Ave., S-215, Chicago 60611
(312)503-0848 fax (312)503-5349
fo...@northwestern.edu
