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CCP4BB  June 2015

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Subject:

Re: Residual density feature

From:

Colin Levy <[log in to unmask]>

Reply-To:

Colin Levy <[log in to unmask]>

Date:

Wed, 17 Jun 2015 10:10:44 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (187 lines)

Dear all, 

Many thanks for the responses received,

To summarise the options for unidentified blobs appear to be:

1. Build something in and define it as a UNL (unknown ligand)

Some debate arose over the specifics of the term ³unknown ligand² and
wether a broader unknown entity description might be more accurate.

2. Leave the difference density and describe the location of the observed
feature using a SITE record.

As my intention was simply to draw attention to the presence of this
feature whilst not implying any identification I have chosen to go down
the latter route and simply leave the difference density for others to
ponder in the future.

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]








On 16/06/2015 18:22, "Dale Tronrud" <[log in to unmask]> wrote:

>-----BEGIN PGP SIGNED MESSAGE-----
>Hash: SHA1
>
>
>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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