Hi,
seeing a "blue" map might at lower sigma levels might give some more
insight. However, there are some caveats in doing so, like solvent
flattening during the refinement. Phenix has options to calculate some
fancy maps, which might give you some more "tips": Feature Enhanced Map,
and Polder map.
Also you mention, that it is a shallow cavity on the surface, that could
mean, that some bigger molecule (PEG, PTPE) is localised only partially.
Or there are multiple states, combined with water etc.... Not helping
much :-)
Do you have an anomalous map available? For example HEPES has a group
with sulphur, which might be seen in anomalous map. If you see anomalous
peaks on sulphurs of your protein, it might not be that unreasonable
even on 1.0A-ish wavelength.
Best regards,
Jan
Dne 06.07.2018 v 16:02 Robbie Joosten napsal(a):
I'd like to add the more current CCP4 solution: AceDRG. It works really well
and you only need to feed it the SMILES string of your compound.
Also keep in mind that many compounds are actually already in the CCP4
dictionary. Finding out whether a compound is, is a two-step procedure:
1) Go to http://ligand-expo.rcsb.org/ and use the search option to find out
whether the compound is already in the PDB
2) If it is, you now have a residue name. To check whether the compound is also
in the CCP4 dictionary, just use the 'Get monomer' option in Coot.
HTH,
Robbie
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
zaigham mahmood khan
Sent: Friday, July 06, 2018 15:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unidentified electron density blob
Hey Uma
Yes, you are right that PFPE is too big for this density. Also, more experienced
scientist in this field has already commented on it.
For the second part of your query, this is how one can generate the
"crystallographic information file" - .cif for the ligand of choice (in case it
is not
available):
1. Using Prodrg server (http://prodrg1.dyndns.org/submit.html)
2. Phenix Ligands (i usually use eLBOW), but this will require smile
strings for the molecules not listed in PDB (and hence 3-letter code is not
available). I use Chemdraw to obtain the Smile Strings..
Best wishes
-Z
Zaigham Mahmood Khan, PhD
Icahn School of Medicine at Mount Sinai
Department of Oncological Sciences
1470 Madison Avenue
New York
On Fri, Jul 6, 2018 at 5:42 AM, Wim Burmeister <wim.burmeis...@ibs.fr>
wrote:
Hello,
a really molecule should show up also in the 2Fo-Fc type map. This
appears not to be the case.
So indeed it is likely that your density corresponds to some alternate
conformation of the surrounding residues present with low occupancy. The
glutamic acid sidechain could be modelled, but I have some doubts about the
rest.
If the refinement is almost finished, it could simply be noise.
Best
Wim
On 03/07/2018 04:23, Uma Gabale wrote:
Dear all,
We came across a blob of unidentified electron density in a
shallow cavity of a bacterial protein structure (pictures attached). It is
surrounded by residues Asp, Arg, Gln, His, Glu, Thr, and Trp.
The protein was expressed in E. coli BL21(DE3) and purified
on Ni-NTA followed by gel filtration. The purification buffers included Tris,
crystallization condition had HEPES and PEG3350; perfluoropolyether was
used as a cryoprotectant.
We would appreciate any help in identifying it.
Thanks and regards,
Uma.
--
Uma Gabale, PhD
Research Associate
Molecular and Cellular Biochemistry
Indiana University Bloomington
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