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On 6/14/2015 2:49 AM, Robbie Joosten wrote:
> Hi Colin,
>
> You can define an UNL (unknown ligand) in the blob. This is the
> standard name for such a compound. It becomes a bit messy in
> refinement in terms of restraints, but it does exactly what you
> want it to do: say you noticed the blob but couldn't figure out
> what it was.
>
There is danger along this route - but I suppose this is a
philosophical matter. Your PDB file is your model for what is in the
crystal. If you don't know what a compound in your crystal is, can
you say that you have modeled it? What are your intentions when you
place this "unknown" residue in your model -- Are you just placing a
marker to tell those who follow that you noticed something here or are
you saying "this is how electrons are arranged here".
Recently I was looking at 1I1W for some reason. It is a very nice
model at 0.89 A resolution. It contains, however, several single atom
residues of type UNX and the atoms are of type X. The problem I have
is that these atoms have their occupancy set to 1.0 and have varying B
factors. What am I supposed to make of a fully occupied atom of
unknown type?
Apparently I'm not alone in my confusion. The Electron Density
Server does not supply a map for this entry. I can see nothing wrong
with the data nor the rest of the model so I presume the service is
failing because it doesn't know how to calculate the scattering of an
atom of unknown type.
So, my question is - If you place marker atoms to indicate the
binding of any unknown ligand, should the difference density disappear
from your map? Certainly if you are interested in bootstrapping phase
information you would want this, but is this appropriate for deposition?
Should you be able to say your difference map is flat and your R value
low when all you did was shrug your shoulders and say "I don't know"?
There is a, sadly underused, feature of the PDB format called the
SITE record. With it you can describe the residues of your protein
that form a binding site and give a text description in a REMARK 800
statement. This option would allow you to acknowledge that something
is binding at this location but leave the difference peak for others
to view and puzzle over on their own.
Dale Tronrud
> Cheers, Robbie
>
>> -----Original Message----- From: CCP4 bulletin board
>> [mailto:[log in to unmask]] On Behalf Of Dom Bellini Sent:
>> Sunday, June 14, 2015 11:36 To: [log in to unmask] Subject:
>> Re: [ccp4bb] Residual density feature
>>
>> Dear Colin,
>>
>>
>>
>> I believe people usually refer to it as "unidentified blob" when
>> depositing/writing in
> these
>> cases. But I wonder whether others may suggest better options.
>>
>>
>>
>> Best,
>>
>>
>>
>> D
>>
>> ________________________________ From: CCP4 bulletin board
>> [[log in to unmask]] on behalf of Colin Levy
>> [[log in to unmask]] Sent: 14 June 2015 09:53 To: ccp4bb
>> Subject: [ccp4bb] Residual density feature
>>
>> Dear all,
>>
>> I am currently working on a structure that contains a residual
>> density feature located
> within
>> the active site. Due to a combination of factors including
>> limited occupancy, modest resolution, twinning etc it has not
>> been possible to unambiguously identify this feature
> despite
>> fairly extensive efforts.
>>
>> What is the best way of dealing with such a feature when
>> depositing the structure?
> Ideally I
>> would like to draw attention to the presence of residual density
>> whilst not implying
> that I have
>> been able to identify it.
>>
>> Many thanks,
>>
>> Colin
>>
>>
>> Manchester Protein Structure Facility
>>
>> Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554
>> [log in to unmask]<mailto:[log in to unmask]>
>>
>>
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