Your pdb-file should contain a line starting with CRYST1 containing cell
dimensions and space group. Maybe this is not the case for your pdb-file?
What is the output of
grep CRYST1 pdffile
where you replace 'pdffile' with the name of the file you are loading into
coot?
Tim
--
Tim
This happens if you try to read a .pdb file from SHELXL into Coot
directly. SHELXL doesn't know the name of the space group (!), only the
symmetry operators (with the advantage that it has no problems with
non-standard settings) so it doesn't put the name of the space group
onto the CRYST1
Another option is refolding which can increase soluble protein content and is
used routinely to achieve soluble protein such as the TIMPs
http://peds.oxfordjournals.org/cgi/content/abstract/7/8/1035
http://www.proteinscience.org/cgi/reprint/11/10/2493.pdf?ck=nck
that said, this is not true of
Hello all,
right, I think I have found a ligand bound to my protein.
I used the COOT utility to find the ligands after reading in a model
and library
file generated by sketcher of my ligand. Now I am a bit unsure as to how to
proceed? How can I 'accept' a state and/or refine it?
Maybe
Don't know if anyone has mentioned this paper but its an exact example how
to make a K channel soluble.
Roosild TP, Choe S.
Redesigning an integral membrane K+ channel into a soluble protein.
Protein Eng Des Sel. 2005 Feb;18(2):79-84. Epub 2005 Mar 23.
PMID: 15788421 [PubMed - indexed for
POSTDOCTORAL RESEARCH ASSOCIATE -
Project Title: Novel Methods for Microcrystal Structure
Determination at NSLS and NSLS-II
Location: Brookhaven National Laboratory, Upton, NY, U.S.A.
This new project is under the direction of A. M. Orville, and is also
associated with the PXRR group
Another reference:
N. Sukumar, Y.Xu, D.L. Gatti, B.Mitra and F.S. Mathews
Structure of an Active Soluble Mutant of the Membrane-Associated
(S)-Mandelate Dehydrogenase
Biochemistry 40,9870-9878 (2001).
In this paper, the membrane protein is converted into the soluble
protein by replacing an
Hi Brenda,
you'll need a cif description file for your ligand which you will read
in either Coot or Refmac so that it will also refine correctly.
I usually get my cif's from the Dundee PRODRG server, you can either
paste your current coordinates as ATOMS in the provided field or sketch
your
We've been having a discussion in the lab about whether or not
middle-sized PEGs such as 4000 can be expected to serve as
cryoprotectants (and if not, why certain commercial kits are
formulated the way they are). Can anybody shed some light /
references on the question of the size of PEGs vs.
Hi All,
As we know, there is a skin on a crystallization drop, especially when the
drop contains PEG. Does anyone know what the skin is, a degraded protein ?
How to prevent it ?
Thanks
Simon
Hi
Try setting up at 4C can help
J
Hi All,
As we know, there is a skin on a crystallization drop, especially when the
drop contains PEG. Does anyone know what the skin is, a degraded protein ?
How to prevent it ?
Thanks
Simon
Hi all，
I want to produce structure-based multiple sequence alignment of my protein
with five of its homologs on DALI server. However, when I tried the Database
Search Form, only one homolog was picked up from PDB. If I align my protein
with each homolog by the DaliLite Pairwise comparison,
You can perform a multiple structural alignment using MUSTANG (
http://www.bx.psu.edu/arun/research/mustang/), which draws upon some of the
underpinnings of the DALI approach.
James
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