On 07/09/2013 07:23 AM, Mark J van Raaij wrote:
> - really the only complicated case would be where a group is covalently linked to more than one amino acid, wouldn't it? Any case where only one covalent link with an is present could (should?) be treated as a special amino acid, i.e. like selenomethionine.
> - groups without any covalent links to the protein are better kept separate I would think (but I guess this is stating the obvious).
>

    Let's consider one of your "simple" cases.  Imagine a heterodimer
(chains alpha and beta) with a single disulfide link between the
peptides.  Do you prefer to have an alpha chain with one residue
being a CYS with an entire beta chain attached as a single residue,
or a beta chain with one residue being a CYS with an entire alpha
chain as a single residue.  Either way you are going to have trouble
fitting into the PDB format's five columns all the unique atom names
for the bloated residue. ;-)

    The problem with this kind of topic is that the molecule is what
it is and it doesn't care how we describe it.  People break the molecule
up into parts to help in their understanding of it and different
people have different needs.  Do you prefer to think of rhodopsin as
containing a LYS residue linked by a Schiff base linkage to retinal
or as having a single, monster, residue with a name you have probably
never heard of?  There is value in both representations depending
on the context.

    A really nice feature of the geometry definitions that have come
out of the Refmac community is that one can define the monster residue
in terms of the LYS-(Schiff linkage)-retinal breakdown.  What hasn't
been done is to create the software that will convert a model from one
form to the other, as the user needs.

    I think this is the direction we should go.  Instead of arguing if,
for example, the "B factor" column should contain the total isotropic
B factor or the residual B factor unfit by the overarching TLS model of
motion, the file supplied by the wwPDB should be a complete,
unambiguous, representation of the model and software should exist
that displays for the user whatever representation they want.  Then the
representation stored in the master repository would not be very
important.

Dale Tronrud

> Mark J van Raaij
> Lab 20B
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> c/Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://www.cnb.csic.es/~mjvanraaij
>
>
>
>
>
> On 9 Jul 2013, at 12:49, Frances C. Bernstein wrote:
>
>> In trying to formulate a suggested policy on het groups
>> versus modified side chains one needs to think about the
>> various cases that have arisen.
>>
>> Perhaps the earliest one I can think of is a heme group.
>> One could view it as a very large decoration on a side
>> chain but, as everyone knows, one heme group makes four
>> links to residues.  In the early days of the PDB we decided
>> that heme "obviously" had to be represented as a separate group.
>>
>> I would also point out that nobody would seriously suggest that
>> selenomethionine should be represented as a methionine with a
>> missing sulfur and a selenium het group bound to it.
>>
>> Unfortunately all the cases that fall between selenomethionine
>> and heme are more difficult.  Perhaps the best that one must
>> hope for is that whichever representation is chosen for a
>> particular case, it be consistent across all entries.
>>
>>                           Frances
>>
>> P.S. One can also have similar discussions about the representation
>> of microheterogeneity and of sugar chains but we should leave those
>> for another day.
>>
>> =====================================================
>> ****                Bernstein + Sons
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>>
>> On Tue, 9 Jul 2013, MARTYN SYMMONS wrote:
>>
>>> Hi Clemens
>>>     I guess the reason you say 'arbitrary' is because there is no explanation of this
>>> rule decision?
>>>    It would be nice if some rationalization was available alongside the values given.
>>> So a sentence along the lines of 'we set the number owing to the following
>>> considerations' ?
>>>    However a further layer of variation is that the rule does not seem to be
>>> consistently applied
>>>   - just browsing CYS modifications:
>>>     iodoacetamide treatment gives a CYS with only 4 additional atoms but it is split
>>> off as  ACM.
>>>     However some ligands much larger than 10 residues have been kept with the cysteine
>>> ( for example CY7 in 2jiv and NPH in 1a18.
>>>     My betting is that it depends on whether something has been seen 'going solo' as a
>>> non-covalent ligand previously so that it pops up as an atomic structural match with
>>> a pre-defined three-letter code.
>>>    This would explain for example the ACM case which you might expect to occur in a
>>> modified Cys.  But it has also been observed as a non-polymer ligand in its own right
>>> so goes on as a separate modification?
>>>     However to be honest I am not sure I have ever seen the rationale for this written
>>> down.
>>>    'Non-polymer' heterogens can turn up either linked or not. Once they are in the
>>> residues they have to make a call on which kind of backbone they will feature in
>>> within the pdb.
>>>    That is why there is  'D5M' for non-polymer deoxyAMP. Also known as ' DA' when it
>>> is 'DNA-linking' but so far not fessing up to life under a third code as
>>> 'RNA-linking'....
>>> Now is perhaps the time to ask for explanations of these nomenclature features before
>>> they become hard-wired in the new pdb deposition system (however there may be time -
>>> I refer you to my previous posting ;).
>>>
>>>   Cheers
>>>      Martyn
>>>
>>> Dr Martyn Symmons
>>> Cambridge
>>> _____________________________________________________________________________________
>>> From: Michael Weyand <[log in to unmask]>
>>> To: [log in to unmask]
>>> Sent: Monday, 8 July 2013, 10:03
>>> Subject: [ccp4bb] modified amino acids in the PDB
>>> Dear colleagues,
>>> We deposited protein structures with modified lysine side chains and
>>> were surprised that the PDB treats the modification as an independent
>>> molecule, with a ?LINK? record indicating the covalent bond ? instead of
>>> defining a modified residue (that?s what we had uploaded to the PDB).
>>> Apparently, anything attached to an amino acid is considered an
>>> independent molecule (and the lysine just called a regular lysine) if it
>>> comprises more than 10 atoms (see below for the PDB guidelines).
>>> I think that?s kind of arbitrary and would give all modified residue
>>> also modified names ? i.e. individual names for all modified lysines, as
>>> it is done for acetyl- or methyl-lysines, for example. I wonder what
>>> other people?s opinion is?!
>>> Best regards
>>> Clemens
>>> ------------------------------------------------------------------------------------
>>> ------------
>>> This is in accordance to the wwPDB annotation guidelines
>>> (http://www.wwpdb.org/procedure.html#toc_2).
>>> "*Modified amino acids and nucleotides* If an amino acid or nucleotide
>>> is modified by a chemical group greater than 10 atoms, the residue will
>>> be split into two groups: the amino acid/nucleotide group and the
>>> modification. A link record will be generated between the amino
>>> acid/nucleotide group and the modification. For modified amino acids and
>>> nucleotides that were not split will follow standard atom nomenclature."