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
>>>>
>>>>
>>>
>>
>>
>
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