In case anyone else happens to look at molecular masses of asymmetric
units in PDB files, here is some enlightenment thanks to help from
Rachel Kramer Green ([email protected]) and Bob Hanson.
This command in Jmol
print {not hoh and model=1 and conformation=1}.mass.sum
reports the molecular mass of the first model's first conformation,
excluding water. A small test case is 3hyd, where the result is 818.99.
The US Protein Data Bank (RCSB) reports a "Structure Weight" (in the
Summary tab of the page devoted to a single PDB entry). It is said to
be the "Molecular weight of all non-water atoms in the asymmetric
unit". In fact, this value excludes models above the first (in
multiple-model PDB files) and confirmations other than the first (in
PDB files with alternate locations for some atoms).
Also very important, it includes atoms that were present in the
crystal but are absent in the model (due to disorder, "missing
non-hydrogen atoms"), and it models in all hydrogens. About 71% of
PDB entries have missing residues (listed in REMARK 465) and 32% have
missing side-chain atoms (listed in REMARK 470). (These values can be
easily obtained with the "Record Name" search field at
http://oca.weizmann.ac.il)
I have suggest to Rachel that RCSB clarify their definition of
"Structure Weight" in the help attached to the value that they report.
In contrast, Jmol reports what is actually present in the model, so
it excludes missing non-hydrogen atoms and missing hydrogens.
Thus, RCSB typically gives a higher value than does Jmol. In the case
of 3hyd, Jmol gives 818.99 while RCSB gives 819.99. I assume RCSB is
adding one hydrogen deemed to be missing, but I haven't identified where.
Eric
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