Thank you for your reply. I don't actually see anything interacting with
what would be the second SH of the DTT. The atom opposite the Cys sulfur
is at a distance of 3.0 A (could this eventually suggest hydrogen
bonding)?? I have been looking at examples in the PDB, and have found a
few protei
Kay Diederichs schrieb:
> Hi Justin,
>
> maybe you would like to put a summary into the CCP4 wiki - just create
> articles "proteins with similar structures despite dissimilar sequences"
> and "proteins with similar function but dissimilar structures", and link
> them to
> http://strucbio.biologie
30% is getting difficult - it may or may not work. But it is worth
trying.
Search model preparation programs such as Chainsaw rely on an accurate
sequence alignment (between model and target), and this also gets
difficult at 30%. You should try something more sophisticated than
simple pairwise ali
Hej Justin,
Have a look at our FISH server (FISH = Family Identification with
Structure-anchored HMMs)
at http://babel.ucmp.umu.se/fish/.
The FISH-server is constructed from a data base of structure-anchored
hidden Markov models, saHMMs,
which are derived from multiple structural superimposi
Dear all,
I am trying to solve the structure of a transcription factor in complex
with its DNA. I got crystals of the complex under different conditions
than the protein alone and they also look different. Unfortunately, they
only diffract to 6Å so far. Before I continue to optimize the crystals
Dear bb,
I have a high resolution dataset showing that the N-terminal threonine
of my protein has been modified and cyclized, with the main chain N and
side chain OG1 now involved in a non-planar 5 membered ring sugar-like
structure. The molecule seems to be 5-6 atoms long with some 'head grou
Hey!
I have found the FFAS server ( http://ffas.ljcrf.edu/ffas-cgi/cgi/ffas.pl )
to build the best models for low homology MR searches. A relevant paper:
2004 Acta Cryst D60 1229-1236.
Best of luck,
Frank
2009/6/21 孙建
> Dear all:
> Recently,I have a problem about molecular replacem
No, there's no cacocylate in the drop, but thanks for the suggestion.
Lynn
MARTYN SYMMONS a écrit :
Dear Lynn - you don't have cacodylate around do you? - there is a DTT
catalyzed modification of Cys by that (several examples in the pdb) -
just a thought.
regards
Martyn
---
Hi Jonathan,
This is purely a chemistry guess, but if you have a PEG400 derived compound
like:
(HO)-CH2-CH2-O-CH2-CHO,
i.e, part oxidised, then the CHO might form a N,O acetal ring with the free
amine and side chain. Five membered ring formation is kinetically
favourable, though the chemistry mi
What about a bit of ethidium bromide, then irradiate with a hand-held uv
light? (assuming that your DNA is ds). Never tried this, but it might work.
Jacob
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laborator
Begin forwarded message:
From: Richard Gillilan
Date: June 23, 2009 9:43:20 AM EDT
To: "Nadir T. Mrabet"
Subject: Re: [ccp4bb] structure <-> function
A very interesting question.
Stephan Jay Gould was well known for his argument that evolution is
contingent on all kinds of factors (like met
Thanks to all who replied regarding experiences with phantom crystals
(objects with crystal-like morphologies but NO diffraction). The
answers were more fascinating than the original poorly worded inquiry
deserved. Here is a recap.
The observation of phantoms may be rare but not so rare: a nu
I would think that a "perfect HCP lattice," no matter the disorder in the
organization of the molecules, would lead to Bragg diffraction, albeit of low
resolution. The "ghost crystals" probably consist of very imperfect lattice(s)
which fluctuate in their dimensions and kind over space and time.
If I understand the idea correctly, I would still expect to see good
Bragg spots, but the amplitudes would represent the rotationally
averaged protein. This is like the hexagonal water lattice (Ih):
there is "disorder" in how the water molecules are oriented at each
lattice point (not reall
Dear Nick,
If you have access to a fluorescent microscope, you can try staining
crystals with PicoGreen and seeing if they fluoresce. (see ref:
Kettenberger H & Cramer P, 2006, Acta Cryst D v62 pp146-150:
Kettenberger H, Cramer P.Fluorescence detection of nucleic acids and
proteins in multi-compo
Note that, despite the claim otherwise in Kettenberger and Cramer, SYBR Gold
does stain at least some proteins, so be sure to run the appropriate
controls.
kmj
On Tue, Jun 23, 2009 at 11:52 AM, Allyn Schoeffler wrote:
> Dear Nick,
>
> If you have access to a fluorescent microscope, you can try
Hi, Kevin,
Wash your crystal very very well to get rid of unbound DNA. Then run
your crystal with SDS PAGE gel, with protein and DNA as markers. After
staining the gel with silver stain, the DNA will show with different
color and migrate about where the dye locates. So don't run too long
time.
Reg
The same goes for other DNA-binding dyes. I've seen a polymerase that binds
EtBr.
-Joel
On Tue, Jun 23, 2009 at 1:38 PM, Kevin Jude wrote:
> Note that, despite the claim otherwise in Kettenberger and Cramer, SYBR
> Gold does stain at least some proteins, so be sure to run the appropriate
>
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