There is no excuse for using MAN to mean both alpha and beta mannose.
It is easy to take a MAN-b-D.cif file and modify it to a BMA.cif. BMA
is already in the monomer library that comes with ccp4 (but I think it
does not have geometry descriptions), and the last time I checked, there
was not a BMA.cif in the default library that ships with phenix.refine,
which makes using the standard beta-D-mannose monomer name one tiny step
more difficult then using MAN for both alpha and beta mannose. No
surprise then that nearly 30% of all sugar entries have incorrect names
and geometries in the PDB (according to the paper that describes PDB-care).
Engin
On 12/22/09 9:29 AM, Damian Ekiert wrote:
For an "ideal" glycan, you could used a model from a high resolution
structure, or something that has been energy minimized, etc. Mostly I
find this helps in getting the sugars in about the right place
(keeping bond lengths and angles reasonable).
I perhaps could stand to fiddle more and maybe I'll look through the
updated documentation. Last I tried, the Asn-NAG1 linkage wasn't
enforced, with would allow the whole glycan to slide down into the
protein, or off into space. I am typically building relatively small
glycans (2-5 residues) into ~3A data, so the density itself doesn't
keep things in place very well.
Regarding BMA vs MAN: When I have tried to used BMA in REFMAC, it
doesn't seem to recognize it and requires a library file. But if you
use MAN, it adds a MODRES record to the header, enforcing beta-mannose
geometry. Not sure if this is just a REFMAC version issue or what.
Best,
Damian
Paul Emsley wrote:
If I can chip into this somewhat sacrilegiously-named thread
1) I *would* use real-space refinement :), specifically Sphere
Refinement. You can dial down the
density weight if needed, of course.
2) the documentation on refining carbohydrates in Coot has recently
been updated
http://www.biop.ox.ac.uk/coot/doc/coot/Refining-Carbohydrates.html
3) Coot does not (yet) correct chiral centre inversions in glycosidic
linkages on refinement
4) or delete the O1s :)
Paul.
Robbie Joosten wrote:
Dear Steve,
I would also use Damian's approach, but the sequence of the core
should be
NAG-NAG-BMA-(MAN)2. This is improtant because the correct
stereochemistry
restraints for beta-mannose can only be applied when you call the
residue
BMA.
Building carbohydrates also comes with special validation requirements.
PDB-care and CARP are both very usefull. Unfortunately, the service is
currently down (http://www.dkfz.de/spec/glycosciences.de). Just make
sure
the links between your carbs are correct and, please, remove the O1
atoms
when needed ;)
Cheers,
Robbie Joosten
----------------------------------------
Date: Mon, 21 Dec 2009 17:48:31 -0800
From: dceki...@scripps.edu
Subject: Re: [ccp4bb] Coot pudding? (a.k.a N-linked carbohydrate
addition)
To: CCP4BB@JISCMAIL.AC.UK
Steve,
My general strategy is to start with an "ideal" glycan (an Asn
linked to
NAG-NAG-(MAN)3 ) and superimpose the Asn on the residue from my
protein.
Then you can move the whole glycan as a rigid body until the Asn and
first NAG are roughly positioned. Then you can tweak any sugars
further
out on the chain to get them to fit. Unless you have really great
density, usually it is best to avoid real pace refine zone. Better to
fit the sugars using the manual rigid body fitting tools, do the best
you can, then REFMAC usually brings them in OK.
I have some models that I could send you if you need them.
Best,
Damian Ekiert
Soisson, Stephen M wrote:
Hi everyone-
I was searching for some information on what might be the best way to
add N-linked sugars in coot, and Google has let me down. Searching
"adding sugars in coot" returns a very nice recipe for Coot Pudding.
***_Recipe for_/ Coot//__/_ Pudding - American_/ Coots/*
******** It has plenty of fat,/
sugar/, and starch, and probably some calcium from the milk.* ...*
The/
coots/ will not tolerate/ adding/ eggs in any form, so this is an
egg*
...*
///_www.beaky_//_*coot*.com/pudding.html_///
///// -/ _Similar_
//
I did not know that coots had such an aversion to eggs. :)
Anyway, would anyone have any top tips on adding N-linked sugars
using
coot? I can import the NAG monomers, but linking them up to the
protein
seems non-trivial
Many thanks in advance,
Steve
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