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Come on, guys, this was a serious question...
A protein should at least be partly ordered in order to get into the
PDB. Obviously, proteins can be partially or totally disordered ("molten
globules"), but I think it is impossible for a protein to be
unstructured in the core while having a structured surface. So yes,
disordered stretches in the PBD, or missing resdues (see REMARK 465 in
the header) are always on the surface.
About the highest B values in the PBD, you'd probably like to know what
is the highest RELEVANT B value entry. This is hard to answer. I've
deposited a structure with a Wilson B-value of 55, with the highest
values (in an outside loop) well over 100. Other crystallographers might
have omitted such a loop from the model, or even have lowered the
occupancy to 0. Their is no specific policy I know of, but there has
been a fairly long discussion on this BB on how to treat these
disordered regions, browse the archives.
Flip
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of
Ian Tickle
Sent: Friday, 23 September, 2005 11:17
To: Ethan A Merritt; [EMAIL PROTECTED]
Cc: [email protected]
Subject: RE: [ccp4bb]: Ends of proteins
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> -----Original Message-----
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
> Behalf Of Ethan A Merritt
> Sent: 23 September 2005 06:15
> To: [EMAIL PROTECTED]; [email protected]
> Subject: Re: [ccp4bb]: Ends of proteins
>
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
>
> On Thursday 22 September 2005 07:00 pm, you wrote:
> >
> > What is the largest B factor that can be registered in a pdb file?
>
> Well, let's see... The PDB file format says B occupies columns 61-66,
> and it's parsed as a real number with format F6.2.
>
> If you actually stuck to that format then the largest value is 999.99,
> but since code is in practice likely to parse this as any legal float
> that fits into 6 columns, I'd bet that most programs would manage to
> read in 99E307 (99 x 10**307).
This would overflow 64-bit IEEE (the max double is
1.7976931348623157E+308) so the best you could manage would be 17E307.
Actually this would be true if the code uses a 64-bit IEEE float to
store the number, but I bet the majority of Xtal software uses only
32-bit, so the answer in practice is probably 340E36 (max float is
3.40282347E+38).
-- Ian
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