Dear Xiang-Jun Lu,
the part of the mmCIF file comes from a loop "_atom_site.group_PDB". According
to the mmCIF dictionary,
" The group of atoms to which the atom site belongs. This data item is provided
for compatibility with the original Protein Data Bank format, and only for that
purpose."
I reckon at the time the PDB file was deposited the policy about what is
considered a HETATM was different to now.
Best,
Tim
On Tue, May 26, 2015 at 01:06:11PM -0400, Xiang-Jun Lu wrote:
> Recently, I came across and was a bit surprised by the different assignment
> of HETATM vs. ATOM records for modified nucleotides in PDB vs. PDBx/mmCIF
> format. Using PDB entry 1ehz (the crystal structure of yeast phenylalanine
> tRNA at 1.93 Å resolution) as an example, 1MA58 in .pdb has atomic
> coordinates listed as:
>
> HETATM 1252 P 1MA A 58 73.770 67.765 34.057 1.00 30.65
> P
> HETATM 1253 OP1 1MA A 58 72.638 67.886 33.105 1.00 32.84
> O
> HETATM 1254 OP2 1MA A 58 73.621 68.229 35.450 1.00 29.49
> O
> ......
> HETATM 1272 C2 1MA A 58 76.527 61.216 38.479 1.00 28.43
> C
> HETATM 1273 N3 1MA A 58 75.793 61.624 37.453 1.00 31.67
> N
> HETATM 1274 C4 1MA A 58 75.142 62.771 37.747 1.00 33.02
> C
>
> and the corresponding section in .cif format is:
>
> ATOM 1252 P P . 1MA A 1 58 ? 73.770 67.765 34.057 1.00 30.65 ? ? ?
> ? ? ? 58 1MA A P 1
> ATOM 1253 O OP1 . 1MA A 1 58 ? 72.638 67.886 33.105 1.00 32.84 ? ? ?
> ? ? ? 58 1MA A OP1 1
> ATOM 1254 O OP2 . 1MA A 1 58 ? 73.621 68.229 35.450 1.00 29.49 ? ? ?
> ? ? ? 58 1MA A OP2 1
> ......
> ATOM 1272 C C2 . 1MA A 1 58 ? 76.527 61.216 38.479 1.00 28.43 ? ? ?
> ? ? ? 58 1MA A C2 1
> ATOM 1273 N N3 . 1MA A 1 58 ? 75.793 61.624 37.453 1.00 31.67 ? ? ?
> ? ? ? 58 1MA A N3 1
> ATOM 1274 C C4 . 1MA A 1 58 ? 75.142 62.771 37.747 1.00 33.02 ? ? ?
> ? ? ? 58 1MA A C4 1
>
> While I have not checked exhaustively, the same inconsistency also occurs
> in several other cases I tested (e.g., 1s72, the Haloarcula Marismortui
> large ribosomal subunit). Has anyone on this list experienced similar issue?
>
> Thanks,
>
> -- Xiang-Jun
>
>
> PS. This is a slightly revised message initially sent to [log in to unmask] on
> Friday, May 22.
>
> Xiang-Jun Lu (PhD)
> Email: [log in to unmask]
> Web: http://x3dna.org/
> Forum: http://forum.x3dna.org/
--
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149
GPG Key ID = A46BEE1A
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