What do you know? The NAG-B-D in ccp4 monomer library is actually N-
acetyl-D-glucosamine, even the description says it is N-acetyl-D-
glucose. After I pulled out the structure from the cif file, I found
it is actually the structure I am looking for but with a wrong name.
So I guess if you can correct the name in this monomer, everything
will be fine. Thanks.
Jianghai
On Mar 1, 2007, at 9:19 AM, Garib Murshudov wrote:
Dear Jianghai
I will add it to library but meanwhile you can create your own
sugar and use it in refinement as external library (if you use
script it is done using libin <library> and there
is a field in the ccp4i for user library)
Garib
On 1 Mar 2007, at 14:07, Jianghai Zhu wrote:
Dear Garib,
NBG is 1-N-acetly-beta-D-glucosamine. However, the sugar
connected to a glycosylation site is actually 2-N-acetyl-D-
glucoamine, which is normally referred as N-acetyl-D-glucoamine
(NAG). The N is connected to C2, not C1, and C1 is actually
connected to ND2 of ASN to form a glycosylation bond. You can get
the high-res structure from HIC-UP and compare them. I would
strongly suggest to add NAG to the monomer library since it is
probably the most common sugar you can find at a glycosylation site.
I think I know why refmac5 didn't take my library. Because of the
glycosylation bond between ASN ND2 and NAG C1, and the bonds
between NAG C1 and NAG O6 (if there are more than 1 NAG), the O1
of NAG is always missing. So the sugar in the structure is always
incomplete comparing to the provided library and refmac5 will try
to pull the description from its own monomer library even the
"make check none" keyword is provided. My questions is how I can
get refmac5 to use my library in this situation. I even tried to
use another unique name for N-acetyl-D-glucosamine and it didn't
work since the sugar structure is always not complete and refmac5
always pulled out the description for N-acetyl-D-glucose from the
monomer library.
If I have to wait until you add NAG to the monomer library, could
you please do it asap? Thank you very much.
Jianghai
On Mar 1, 2007, at 8:06 AM, Garib Murshudov wrote:
Have you looked at NBG it seems to be N-acetyl-beta-D-glucosamine
Garib
On 28 Feb 2007, at 23:13, Jianghai Zhu wrote:
Dear Dr. Murshudov,
I have some N-acetyl-glucosamine (NAG) in my structure. When I
searched the monomer library in CCP4 6.0.2, I found out that NAG
is actually N-acetyl-glucose, which is much less common, I
believe. I downloaded the high-resolution structure of N-acetyl-
glucosamine from HIC-UP and used sketcher to generate a cif
library. I named the sugar NAG. I read this new cif file into
refmac5 (5.3) and used "make check none" in the refinement. I
thought my library would overwrite the NAG in the monomer
library in CCP4, but refmac5 still use the NAG it found from
the monomer library. Is there anyway to make sure refmac5 will
use my library even there is another one in the monomer library
with the same name?
Ethan Merritt told me that N-acetyl-glucosamine was in the
monomer library a few versions back. But I could not find it
anywhere.
Thanks.
Jianghai
