These dodecins are a good examples:
PDB 2V21 and the like
The dodecin from Thermus thermophilus, a bifunctional cofactor storage protein.
Meissner, B., Schleicher, E., Weber, S., Essen, L.-O.
Journal: (2007) J.Biol.Chem. 282: 33142
PubMed: 17855371
DOI: 10.1074/jbc.M704951200
Good luck
Harm
I have a question about B-factors and occupancies of side chains - I am working
on a 2.8 A structure which is missing density for some of the side chains
(especially the floppy ones like Lysine/Argenine, Glutamine) in loop regions
and the B-factors for these side chains are over 100.
I was
I usually leave them in although their position is so uncertain; they
probably have multiple conformations but that is hard to model at 2.8A .
But that is not a hard and fast rule - lots of people set the occupancy to
0.00 and check whether the later maps give better guideance..
Eleanor
On 21
Dear Urmi,
This has been the subject of long-threads in the past and belongs to the
same category as the yearly linux vs. Mac discussions. By searching the
archives, you should be able to get all the information you want, and
even more!
Here is my (personally biased) summary:
Lowering the
Dear all,
What's the correct way to build and refine sugar polymers?
I am currently building several structures with different kinds of sugar
polymers bound to them.
Searching for similar ligands in the PDB, I end up with e.g.
trisaccharides that are named as one molecule, even though they are
Dear Folmer,
I build them from monomers like NAG, MAN, FUC etc. It used to be quite
messy (reason why people put in triscaccharides??) but works fine
nowadays. You have to put in LINK records to specify the connections and
remove the oxygen which gets replaced by the link (usually O1). There
Concerning the naming as one molecule: the sugar monomers get the same
chain ID as the protein they are connected to and arbitrary residue
numbers. I usually start numbering from 1000 to prevent overlap with the
numbering of the amino acids.
HS.
From:
We might have just found a new recurring discussion - what to do with insertion
codes! I am sure the opinion split is close to 50/50.
Personally, I don't think insertion codes make sense in the first place. Are
catalytic triad residues always the same distance from the N-terminus? No. The
Posted on behalf of Prof. Daan van Aalten
Dear all
I have two postdoctoral and one technical position(s) available in my research
group, as listed below. Please apply through the mechanisms indicated although
happy to discuss things informally via email. Candidates who in parallel are
willing
Dear Ed,
I do not think there is any split opinion as far as users are concerned:
Programs that pay attention to insertion codes will also handle regular
pdb files correctly so nothing changes for the users. The advantage is
that in the odd case one loads a vintage pdb file with insertion codes,
Hi Folmer,
Just to add some tips:
Concerning the naming as one molecule: the sugar monomers get the same
chain ID as the protein they are connected to and arbitrary residue
numbers.
I usually start numbering from 1000 to prevent overlap with the numbering
of the amino acids.
1) Just don't
Hi all
Thank you all for your replies.
I might have expressed myself poorly, but I am not talking about covalently
linked sugar modifications, so for my purpose there's no need to be
concerned about insertion codes ;-)
The glycosciences.de link is really useful. There does not seem to be a
test
Hi Folmer,
RAF is in the PDB ligand dictionary with status 'REL' so you can use it. If
RAF is a subset of something bigger, then perhaps you should use
monosaccharide building blocks. If in doubt, ask a PDB annotator.
Anyway, PDB-care will check whether the connectivity in a compound named RAF
Dear CCP4 Users
A CCP4 update has just been released, consisting of the following changes.
* Geomcalc: io bug fixing in residue numbering
* Pisa: fixes for handling back slashes on windows
* Aimless: fixes in Define Run section of the aimless task interface
* Ample/MrBUMP: now runs shelxd_mp in
Hi all-
Sorry if this has been gone over before but I could not find a direct answer
after a cursory search in the archives and online. Is the CCP4 suite compatible
with Mountain Lion? Specifically, the GUI (ccp4i) and Coot? Our Macs are
running Leopard and Snow Leopard and we've been thinking
Hi Brad, everything is working fine, both on laptop (Macbook pro) and
PowerMac.
Best regards,
Albert
2013/2/21 Brad Bennett bradbennet...@gmail.com
Hi all-
Sorry if this has been gone over before but I could not find a direct
answer after a cursory search in the archives and online. Is the
All works fine. You'll need to install XQuartz (Apple are no longer supplying
their own X11 builds) but that's just a couple of clicks in the box that pops
up the first time you run an program that needs X.
The (on by default) versioning auto save is a PITA if you ever use textedit to
edit
Dear Colleagues,
Dr. Adrian Gross’s lab at Chicago Medical School (Rosalind Franklin University
of Medicine and Science) has an opening for a post doctoral fellow position to
study the structural and functional properties of different mammalian and
bacterial potassium channel proteins using
Tenure Track Position in the College of Medicine
at the University of Saskatchewan
The College of Medicine invites applications for a tenure track faculty
position at the Assistant, Associate or Full Professor level in the area of
structural biology of membrane proteins, or in the application
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