Dear Anita,
Sometimes the protein of interest has a relatively strong inherent binding
affinity to the IMAC
column. Have you tried to bind the cleavage reaction to an IMAC column
and then elute using a shallow imidazole gradient?
In fact, Porath developed IMAC chromatography as a tool for prote
Thanks everyone for your suggestions !
Artem has pointed out that low diffraction of the crystal might be because
of other problems .. If you could* highlight a bit more on this issue it
would be helpful for me.*
I have tried to seperate the cleaved, uncleaved and TEV over MonoQ column
but there w
We are pleased to announce the 18th Summer School in Protein Crystallography to
be held this year at St Andrews from 3rd – 9th September.
Further details and an on-line application form can be found at:
http://www.st-andrews.ac.uk/~glt2/PX2011
Best wishes
Garry Taylor & Jim Naismith
Biomedi
First three numbers are the Euler angles. The next 3 are the
(approximate) centre of mass of the source molecule. The last 3 are the
corresponding point in the target molecule.
(This is a little more complex than the form used in 'dm', but
unfortunately the simpler form was missing important i
Dear CCP4BB members,
We are using a script written in python to generate symmetry mates for a
given pdb file using PYMOL. After generating symmetry mates we want to
combine all the symmetry molecules in a single PDB file with all the chains
having unique chain IDs. Since all the symmetry mates
MOLEMAN from the Uppsala Software Factory
by Gerard Kleywegt of course
It is easy as to say " Do it!"
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-edito
I wrote a little utility called pdb_merge that is in CCP4. With the
"nomerge" option, it checks for duplicate chain IDs, and renames chains
if necessary.
The main limitation is that it can only merge 2 files, but you should be
able to script a loop to call it multiple times.
What happens if you h
Hi Kenneth,
> I know that TLS is a group B factor for regions of proteins that are moving
> the same.
You have to be a bit careful here: first B factors do not necessarily
imply motion, they imply displacement (i.e. it could mean static
displacements which just vary between unit cells). That's
Hi Anita,
Admittedly, there are proteins that naturally bind to Ni-NTA so tightly that
they co-elute with our His6-tagged proteins even on an imidazole gradient.
However, we do need some luck to come across a protein with such property. For
most proteins, they would just flow through the Ni-NT
You could also try upping the tev:prot ratio, such that the protein is
~100% cleaved, then do IMAC or simply some other, non-IMAC
chromatography step, such as ion exchange or SEC, depending on the
size and charge of your protein relative to TEV.
JPK
On Fri, Apr 8, 2011 at 8:17 AM, Zhijie Li wrot
Does anyone know what the record is for "most reflections per atom?"
JPK
On Fri, Apr 8, 2011 at 8:06 AM, Ian Tickle wrote:
> Hi Kenneth,
>
>> I know that TLS is a group B factor for regions of proteins that are moving
>> the same.
>
> You have to be a bit careful here: first B factors do not ne
I'd say since you obtained crystals with your tag it is not a disturbing factor
and either disordered or making contacts. So removing the tag you might end up
not getting crystals in the worst case. Now to the question why they don't
diffract. Did you test the old fashioned way at RT in capillar
pdbset does this nicely:
pdbset xyzin mono.pdb xyzout dimer.pdb <
MOLEMAN from the Uppsala Software Factory
by Gerard Kleywegt of course
It is easy as to say " Do it!"
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel
Krishan,
Here is a simple stand-alone python script that should do what you want.
Greg
#!/usr/bin/python
#
# rechainpdb.py
# usage:
# python rechainpdb.py mypdbfile1.pdb mypdbfile2.pdb mypdbfile3.pdb
#
# This will generate a new file with all pdbfile (ATOMs and HETATMs) in a single
# file, with e
On Friday, April 08, 2011, Jacob Keller wrote:
> Does anyone know what the record is for "most reflections per atom?"
It goes up as high as 300 reflections per modelled atom in some
virus structures modelled with strict NCS.
There's one outlier in the current PDB set with >1000 refls/atom.
Hi all,
I've been getting blocked running minimize/optimize from tinker. The issue is
atom types and energy parameters. For small molecules, I can hand check the
types and get tinker to complete successfully. However as my molecules get
larger (and I'm attempting to automate a screening proto
Thanks to everyone for their suggestions. The closest solution was
1. Expand dataset in P1 using SFTOOLS (keyword EXPAND)
2. Write it out in text file
(WRITE data.hkl format(3i5,2f16.3) col col1 col2)
3. Use program HYDENS (Bart Hazes)
It should be noted that the current version of HYDENS o
Hello all,
Given a PDB file of a newly solved protein structure, what is the standard
procedure for assigning regions of secondary structure? And by this I mean
to ask, how does one decide which residues form beta strands, which alpha
helices, and so on? Is DSSP sufficient for this? Are we supp
First, I don't think glycosylation occurs on lysine residues.
You should try to crystallize it as is, if that doesn't work, try to
remove the glycosylation with some or all of the following: EndoH,
PNGaseF, EndoF1, EndoF3. We have used them all to various degrees of
efficiency to remove glycans f
Hi Bei,
First of all, I think you meant N-linked glycans, and the following discussion
are based on this assumption. I am not aware of any direct glycosylation on
lysines except for the O-glycosylation of hydroxylysines, which is really rare.
1. If you have enough protein, you should screen b
You may also want to have a look at this summary of a 2006 discussion:
http://www.mail-archive.com/ccp4bb@dl.ac.uk/msg01697.html
From: joybeiyang
Sent: Friday, April 08, 2011 2:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] off topic: Is deglycosylation necessary for crystallization?
D
Just use dssp and cite it. For cartoon figures, if you provide a disclaimer, it
doesn't hurt to tweak it a bit to make it look better.
The idea is that readers are supposed to know that a protein doesn't really
look like a cartoon--and those who don't understand the distinction probably
won't h
Hi Ed,
thanks for nice summary! Just a quick update while on this subject:
(using nightly build dev-724 an up) you will be able to get density value at
a given point using just one command:
phenix.map_value_at_point map_coeffs.mtz label="2FOFC" point="1 2 3"
point="4 5 6"
where you can specify
Hi Anita,
so you tested your crystals inhouse, any idea how they do at the synchrotron ?
Still no diffraction ?
Since it's a hexamer I would expect the His-tag to be not so important and
would rather rescreen with seeding first to see if any other conditions might
result in diffracting crystals
24 matches
Mail list logo
