El 16/02/12 05:06, Xun Lu escribió:
> Hi Lisa,
>
> Please go check your PDB file. Are those bases written out like "DT" or
> "THY" or "Td". Coot recognizes certain format for DNA bases but I forgot
> which one coot likes. I don't have my laptop with me right now. My
> guess would be "Td". :)
>
Hi Lisa,
I will second James' suggestion. DNA packing seems really important, and
making the DNA length as X half turns is usually good for packing (X=2, 3,
4 ...).
Another thing you might want to try is Hoogstein base pairing.
Cheers,
Xun
On Wednesday, February 15, 2012, James Stroud wrote:
>
Hi Lisa,
Please go check your PDB file. Are those bases written out like "DT" or
"THY" or "Td". Coot recognizes certain format for DNA bases but I forgot
which one coot likes. I don't have my laptop with me right now. My guess
would be "Td". :)
Best,
Xun
On Wednesday, February 15, 2012, LIS
Jacob,
I wish it were that cheery. Do not forget the darker side of history.
The prefix "L-" stands for levorotary. The "levo" comes from the Latin wording
for "left side". Left handedness is also known as sinistrality, from the Latin
"sinistra" which also meant the left side, but over time
G-d is right-handed, so to speak:
Ex 15:6 "Thy right hand, O LORD, is become glorious in power: thy
right hand, O LORD, hath dashed in pieces the enemy."
Since we are made in His image, and our (chiral) molecules are the
cause of making most of us right-handed, which enantiomer to use was
not a r
Well if you think about it technically God produced plants within three
days which if far too little work for a thesis. Maybe it could count as
preliminary results for one aim of a thesis proposal so it might be enough
to get PhD candidacy depending on how demanding your committee is. You
could alw
Diffracted intensity goes up by the cube of the wavelength, but so does
absorption and I don't know exactly about radiation damage. One
interesting point is that on image plate and CCD detectors the signal is
also proportional to photon energy, so doubling the wavelength gives 8
times diffract
Acta Cryst. (1997). D53, 734-737[ doi:10.1107/S0907444997007233 ]
The Ultimate Wavelength for Protein Crystallography?
I. Polikarpov, A. Teplyakov and G. Oliva
http://scripts.iucr.org/cgi-bin/paper?gr0657
may give some insights.
To the OP, have you solved the structure? In some cases, s
Well, but there is more scattering with lower energy as well. The
salient parameter should probably be scattering per damage. I remember
reading some systematic studies a while back in which wavelength
choice ended up being insignificant, but perhaps there is more info
now, or perhaps I am remember
No impact ? Longer wavelength more absorption more damage. But between the
choices given no problem.
Spread of spots might be better with 1.0 versus 0.9 but that depends on your
cell and also how big your detector is. Given your current resolution none of
the mentioned issues are deal breakers.
I would say the better practice would be to collect higher
multiplicity/completeness, which should have a great impact on maps.
Just watch out for radiation damage though. I think the wavelength
will have no impact whatsoever.
JPK
On Wed, Feb 15, 2012 at 4:23 PM, Seungil Han wrote:
> All,
> I am
If you agree, please signing the petition below. You need to register on
the link below before you can sign this petition. Registration and signing
the petition took about a minute or two.
Cheers,
Raji
-- Forwarded message --
From: Seth Darst
Date: Tue, Feb 14, 2012 at 12:40 PM
S
Hi Jacob:
After giving this a great deal of reflection …..
I realized that you would face the same paradox that
God had to resolve six thousand years ago at the Dawn of
Creation, i.e., He needed D-deoxyribose DNA to code for L-amino acid
proteins, and vice versa. Likewise, you would probably be f
Weds., Feb. 15th 2012
EBI
Good evening,
PDB entries with spg P 1- or I -4 C 2 are
3al1 3boi 2gpm 1krl 2gq7 2gq6 2gq5 2gq4 2g32 1pup 3e7r 1vtu 3odv 3trw
3try
you can get information on each from pdbe
pdbe.org/entry
i.e.
pdbe.org/3al1
etc.
Miri, PDBe
On Wed, 15 Feb 2012, Jacob Keller wrote:
All,
I am curious to hear what our CCP4 community thoughts are
I have a marginally diffracting protein crystal (3-3.5 Angstrom resolution)
and would like to squeeze in a few tenth of angstrom.
Given that I am working on crystal quality improvement, would different
wavelengths make any differenc
I feel compelled to throw a few references into the ring.
NFAT is a protein where you get a good sampling of snapshots:
1. Folded up as a monomer when interacting with partner proteins:
http://www.ncbi.nlm.nih.gov/pubmed/9510247
http://www.ncbi.nlm.nih.gov/pubmed/16873067
2. Extended as a
The structure of an all D-amino acid version of the HIV-1 protease was
solved in 1992 (see Milton, Milton, and Kent, 1992, Science,
256:1445-1448). The D-enzyme was seen to have a structure that is the
mirror image of the L-enzyme, and showed specificity for the enantiomeric
form of the chiral subs
Dear Crystallographers,
thanks for all of the responses and conversation. I have culled
together the various references which have been sent on the BB and
which I have come up with, and posted them below. Worthy of special
mention, I think, is the first one (Lange et al), in which 46 (!)
different
Right on the money!
JPK
On Wed, Feb 15, 2012 at 12:28 PM, David Schuller wrote:
> On 02/15/12 12:41, Jacob Keller wrote:
>>>
>>> Are there any all-D proteins out there, of known structure or
>>> otherwise? If so, do enantiomer-specific catalyses become inverted?
>>>
>>> JPK
>>>
> I looked a lit
So who out there wants to start an all-D microbial culture by total
synthesis, a la the bacterium with the synthetic genome a while back?
Could it work, I wonder? I guess that would be a certain benchmark for
Man's conquest of nature.
JPK
ps maybe if there is a broadly-acting amino-acid isomerase
On 02/15/12 12:41, Jacob Keller wrote:
Are there any all-D proteins out there, of known structure or
otherwise? If so, do enantiomer-specific catalyses become inverted?
JPK
I looked a little harder, and at least one D-enantiomeric protein was an
enzyme:
Total chemical synthesis of a D-enzym
On 02/15/12 12:41, Jacob Keller wrote:
Are there any all-D proteins out there, of known structure or
otherwise? If so, do enantiomer-specific catalyses become inverted?
JPK
What do you mean by "Out There"? If you mean in the PDB, then yes. As
of two weeks ago, there are ~ 14 racemic structures
Building on Alex's suggestion, here are some papers on rationally engineering
new crystal contacts:
via disulfides:
http://www.pnas.org/content/103/44/16230.long
http://onlinelibrary.wiley.com/doi/10.1002/pro.550/abstract;jsessionid=783A91
CC93571B0348F37A325929676D.d01t02
or via leucine
The most famous case I know of was the HIV protease. My grad school PI used
to use it as an example in class.
Science. 1992 Jun 5;256(5062):1445-8.
Total chemical synthesis of a D-enzyme: the enantiomers of HIV-1 protease
show reciprocal chiral substrate specificity [corrected].
Milton RC, Milton
Are there any all-D proteins out there, of known structure or
otherwise? If so, do enantiomer-specific catalyses become inverted?
JPK
On Wed, Feb 15, 2012 at 8:05 AM, David Schuller wrote:
> Wukovitz & Yeates (1995) Nature Struc. Biol. 2(12): 1062-1067
> predicts that the most probable space gro
You can also try putting a different affinity tag on the other
terminus, and use that as a second step.
JPK
On Wed, Feb 15, 2012 at 11:25 AM, Xiaodi Yu wrote:
> Hi Sivasankar:
>
> Are you sure it is due to the protein degradation? Maybe you can try to do a
> western blot or others to check if it
Hi Sivasankar:
Are you sure it is due to the protein degradation? Maybe you can try to do a
western blot or others to check if it is the product of degradation. By the
way, where you put the 6 histag, N- or C-terminal? If it is at the N terminal,
maybe it is the truncation version of your prot
try experimenting with different, especially protease-deficient, E coli strains
to express the protein and try different methods to lyse the bacteria
(sonication, french-press, emulsification, bead-beater, mortar & pestle under
liquid nitrogen).
on the other hand, if you are lucky, you are just
Hi,
you may also check things like chemical degradation in SDS buffer as part of
the analysis. Esspecially your degradation pattern is very much constant
throughout your whole purification procedure.
Christian
Am Mittwoch 15 Februar 2012 14:09:19 schrieb Sivasankar Putta:
> Dear All,
>
> Can
Hi Laurie,
Not much, I did not get any useful feedback so I emailed Paul Emsley
directly.
Chris
On Tue, 2012-02-14 at 22:43 -0500, Laurie Betts wrote:
> Problem with COOT and MSE (SeMET ) residues
--
Dr. Christopher Browning
Post-Doctor to Prof. Petr Leiman
EPFL
BSP-416
1015 Lausanne
Swit
Wukovitz & Yeates (1995) Nature Struc. Biol. 2(12): 1062-1067
predicts that the most probable space group for macromolecular
crystallization is P -1 (P 1-bar). All you have to do to try it out is
synthesize the all-D enantiomer of your protein and get it to fold properly.
On 02/14/12 18:36, Pr
Late induction for short time. Then immediately purify it cut down on any
unnecessary steps eg shorter spin all on ice or coldroom etc.
Jürgen
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria R
Alternatively, why not do a quick polish step using a long gradient on a 5
mL anion or cation exchange column, followed by a gel exclusion cleanup if
necessary? Once the proteases have been removed from the crude extract,
further degradation of purified protein should be minimal. This
purification
Dear all,
i am quite new to refinement and after refinement using refmac i have a
resonable R-factor and R-free (22 and 27%), but Molprobity analysis shows
c-beta devaition s as 23.
How can i fix this?
--
B. Anuradha
Research scholar,
CAS in crystallography and Biophysics,
University of Madras.
You can try the scripts
user-define-restraints.scm/user_defined_restraints.py which allow you to
specify restraints. These are not available in the distribution (yet)
but from google code:
http://code.google.com/p/coot/source/browse/trunk/scheme/user-define-restraints.scm
http://code.google.co
Dear CCP4bb,
Is there any way to define a hydrogen bond as a restraint for real space
refinement in Coot? It would be really useful for e.g. nucleotides where
you might hypothesize or know that specific hydrogen bonds are formed.
Sincerely,
Morten
--
Morten K Grøftehauge, PhD
Pohl Group
Durham
EMBO practical course on Solution Scattering from Biological Macromolecules
The course will take place at EMBL Hamburg, Germany, on October 17-24, 2012.
Organizers:
D. Svergun, M. Roessle, M. Petoukhov, A. Kikhney (European Molecular
Biology Laboratory, Hamburg Outstation)
The course aims at
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Hello Lisa,
which version of coot do you use? Maybe it is outdated and that function
not yet properly implemented. I can confirm Bill's comment, and we work
with coot 0.6.2.
Cheers,
Tim
On 02/15/2012 09:01 AM, LISA wrote:
> Hi all,
>
> I am refinin
Dear All,
One of the most efficient methods to change space group and packing
without having to change
the sequence is to change the length of N and/or C terminal tags.
An example that I am familiar with is given by the following PDB codes.
1JIZ, 1RMZ, 1JK3, 1UTT, 1UTZ, 2WOA, 2W0D, 1ROS, 1O
This paper is a favorite:http://www.ncbi.nlm.nih.gov/pubmed/2160019
J Mol Biol. 1990 May 5;213(1):159-66.
Crystallization of Escherichia coli catabolite gene activator protein with its
DNA binding site. The use of modular DNA.
On Feb 15, 2012, at 12:06 AM, LISA wrote:
> Hi all,
>
> I ha
Use 5' overhangs of two and make the DNA 10, 11, 15, 20, 21 25, 26, 30, or 31
bases in length. Count the overhangs in the length.
If you don't know where to start, try 15, 25, and 26 first because they will
make 2(1) screws, which are good for crystals.
James
On Feb 15, 2012, at 1:06 AM, LISA
Lisa, there isn't unfortunately a hard and fast rule for the length of DNA used
in co-crystallisation. It usually is just a case of screening different
lengths, permuting the sequence, and investigating overhangs or gaps in the DNA
duplex. We generally work with oligos between 8 and 21 nts in l
Hi all,
I have a DNA binding protein. I can get crystals when I mix 8-28 nt dsDNA
with my protein. But neither of them has good diffraction. Some biochemical
data said the longer of DNA, the tigher of the binding betwwen DNA and my
protein. The binding is not sequence-specfic. Does anyone have sug
Hi all,
I am refining a structue of protein-DNA complex with coot. I add DNA by
"adding ideal DNA/RNA" in the other model. But I cannot edit chi angle of
these nucletide, neither the mutate. When I press the mutate and my DNA,
coot give amino acid not nucletide. Why?
Thanks
Lisa
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