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 pd...@sdsc.edu on > Friday, May 22. > > Xiang-Jun Lu (PhD) > Email: xiang...@x3dna.org > 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
