Dear Paul (both),
Thanks a lot! Now it worked!
The Cys is at the active site/ binding pocked of a designer enzyme, which
actually originally was drafted into the scaffold of a carbohydrate binding
enzyme.
Best wishes,
Joël
Joël Bloch
Postdoctoral fellow
Group Prof. Locher
Institute of
Dear Chitra,
Crystallizing both proteins together is a very good idea: If you get a
structure, it will be an interesting one, even if the C-terminus remains
invisible.
Concerning the flexible C-terminus: is it the linker linking the second domain
to the first one? In that case it might just
Dear Klemens,
I am going to setup the crystallisation of the entire protein anyhow. I
hope I get lucky :)
Thanks
Chitra
On Thu, Mar 12, 2020 at 5:12 PM Klemens Wild <
klemens.w...@bzh.uni-heidelberg.de> wrote:
> On 12.03.20 08:53, chitra latka wrote:
>
> Dear All,
>
> I am working on a protein
Hello,
B-factors actually do have a physical meaning which is at least to some
extent reflected by the crystal structures as refined. This can be
demonstrated at higher resolution structures: when we created three
tiers of structures, better than 1.9 Å, 1.9-2.4 Å, and 2.4-3.0 Å,
structures
Dear Herman,
Its a two domain protein and the second domain gets chopped off and
stabilises the other domain by binding near the flexible C - terminus of
first domain. I am trying to crystallise both the proteins together.
Literature review doesn't report binding of the protein to any other
Hi Chitra Latka,
By far the best approach is to find what protein is interacting with the one
you have the structure and try co-crystallizing them together. At least there
will be some more biology (science) involved in what you will be doing. You may
get lucky and get different packing of
On 12.03.20 08:53, chitra latka wrote:
Dear All,
I am working on a protein that has flexible C terminus. None of the
available structures even in homologs have density for C term region
(around 20 odd residues). All the available pdb entries have missing
density for these 20 residues at C
Hi Joel,
The red trapezoids are indicative of cis-peptide bonds that are exceptionally
rare, and usually indicate incorrect tracing of the backbone (unless you have
good enough data to unambiguously decide that a cis-peptide bond is correct).
I'm afraid I don't know how to get rid of them,
Hi Dave
Thanks a lot for the hint. The Cis-bond should be correct, as it is a buried
glycine residue in a crystal structure at 0.95 Å resolution.
But it would be great, if there would be a way to simply hide the cis-bond
warning. I would like to generate a supplementary figure with a broad
Hi Joël,
You can go to Calculate -> Scripting -> Python and enter:
set_draw_cis_peptide_markups(0)
Kind regards,
Paul
On Thu, 12 Mar 2020 at 09:58, Joël Bloch wrote:
> Hi Dave
>
> Thanks a lot for the hint. The Cis-bond should be correct, as it is a
> buried glycine residue in a crystal
Hi,
I think through bond and through space B factor (+ sphericity) restraints
primarily exist for pragmatic reasons: they are needed to maintain the
numerical stability of the refinement. That is a separate issue from making
physical sense. If one finds consistent B-factor similarity in atoms
Dear CCP4 community,
Is there any way in Coot 0.8.9.2 to remove/hide the red trapezoids that are
indicating planar bonds?
I couldn’t find anything on that, neither in the manual nor FAQ.
Thanks a lot for your help!
Best wishes,
Joël
On 12/03/2020 09:14, Joël Bloch wrote:
Is there any way in Coot 0.8.9.2 to remove/hide the red trapezoids that are
indicating planar bonds?
I couldn’t find anything on that, neither in the manual nor FAQ.
(Good for you for reading the documentation)
The red trapezoids represent cis
Dear Chitra,
There usually is a reason the C-terminus is disordered. Either it needs to bind
a ligand to get ordered, or it needs to bind to some other protein. You have to
check the literature. If the C-terminus binds a ligand, you have to add this
ligand to your crystallization experiment.
Dear All,
I am working on a protein that has flexible C terminus. None of the
available structures even in homologs have density for C term region
(around 20 odd residues). All the available pdb entries have missing
density for these 20 residues at C terminus.
I am going to try my luck
All good points in the contributions from Alexis and Randy.
To confirm Alexis’ interpretation of my previous post, my main concern about
the ½ bit threshold for “nominal” resolution was that it is in danger of being
adopted independently of the requirement (for example by those doing x-ray
Hi Jacob,
On Thu, Mar 12, 2020 at 9:13 AM Keller, Jacob
wrote:
> I would think the most information-reflecting representation for
> systematic absences (or maybe for all reflections) would be not I/sig but
> the reflection's (|log|) ratio to the expected intensity in that shell
> (median
Hi Chitra,
To add to the discussion, I can offer an example about obtaining the
structure of a flexible/disordered N-term of a membrane protein.
Previous structures of the full-length multidrug efflux transporter AcrB
(12 TM helices in each protein ~1000 residues, forms a trimer, so 36 TM
Hi Chitra,
Sometimes disorder ‘is’ the functional state of a peptide segment, and in those
cases, if you see the segment ordered in your crystal structure, it is not
physiologically relevant; rather it is a result of crystal packing. Sometimes
disordered segments undergo a folding when they
Dear Chitra,
Try adding a ligand to the crystallization. This worked for us with ALDH7A1:
https://www.ncbi.nlm.nih.gov/pubmed/26260980
ALDH7A1 is an example of an enzyme with a flexible C-terminus (11 residues).
The conformation of the C-terminus depends on the presence of a ligand in the
I would think the most information-reflecting representation for systematic
absences (or maybe for all reflections) would be not I/sig but the reflection's
(|log|) ratio to the expected intensity in that shell (median intensity, say).
Thus, when the median intensity is 1000 counts, and one
Dear all,
I would like to remind you that we are still looking to fill a postdoc position
at AstraZeneca (Cambridge UK) in collaboration with Prof Ashok Venkitaraman's
group at the MRC Cancer Unit. This is an opportunity for a talented and
self-motivated structural biologist to undertake
Hi David and James,
Thank you for your kind response. Blend is working now.
Ravikumar.
On Fri, Mar 6, 2020 at 1:15 PM David Waterman wrote:
> Dear Ravi Kumar
>
> If I remember correctly, Blend requires the path to the executable Rscript
> rather than R. I can't check this now but I can
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