All entries list atoms starting at the N-terminus (or 5') so
connectivity goes in the order of the atoms in the file -
obviously with the possibility of unconnected portions
where the density is inadequate.
The entire philosphy of allowing numbering other than 1 - N
had to do with preserving relationships with other proteins.
The most common use relates to having an initial sequence 1 - N
and then a similar sequence from another species with insertions
and/or gaps. People wanted to be able to talk about the active
site (which was preserved) using the same residue numbers.
Negative numbers came up with additions at the N-terminus.
Offhand, I don't recall why descending numbers were used but
I believe that there is at least one such entry.
Frances
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On Fri, 19 Sep 2008, Ian Tickle wrote:
But what connectivity would be implied by descending numbers: the order
in the file or the order of the numbering? I assume the former,
otherwise what would be the point of having descending numbering? And I
wonder how many programs would baulk at it (or even at ascending
negative numbers?).
-- Ian
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On
Behalf Of Frances C. Bernstein
Sent: 19 September 2008 16:44
To: Todd Geders
Cc: [email protected]
Subject: Re: [ccp4bb] Non-sequential residue numbering?
As long as each residue within a chain has a unique identifier
(residue number plus insertion code), there is no restriction
on numbering. The numbers can be in ascending or descending
order, non-sequential, and even negative.
Frances
=====================================================
**** Bernstein + Sons
* * Information Systems Consultants
**** 5 Brewster Lane, Bellport, NY 11713-2803
* * ***
**** * Frances C. Bernstein
* *** [EMAIL PROTECTED]
*** *
* *** 1-631-286-1339 FAX: 1-631-286-1999
=====================================================
On Fri, 19 Sep 2008, Todd Geders wrote:
Hello all,
I have a structure from a non-natural fusion of the truncated
C-terminus
of
one protein with the truncated N-terminus of another. For the
deposition, we
want to keep the numbering as found in the separate proteins. It
looks
something like this:
1 12
| |
....HWVCKDIALLMCFFLEEMSEEP....
| |
754 763
At no point is there an overlap in numbering (i.e. the N-terminal
residue
number is higher than the C-terminal residue number).
Is this numbering scheme supported by the PDB standard? Thus far,
all
of the
software seems to handle it (refmac, Coot, PyMOL, pdb_extract, PDB
precheck &
validation, etc).
Can anyone see a reason to not deposit with this non-sequential
residue
numbering?
~Todd
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