During a routine search of the public PDB_REDO
database (Joosten et al.
) for a crystal structure model of birch pollen protein Bet v 1, a significant discrepancy between the originally reported R
= 0.298, R
= 0.274) and the conservatively re-refined structure of PDB entry 3k78
(Bet v 1d) was detected (0.177, 0.126). These R
values are unexpectedly low for a 2.8 Å structure. At the same time, the electron-density map provided by the Uppsala Electron Density Server, EDS (Kleywegt et al.
), publicly accessible through the PDBe (Velankar et al.
), shows numerous side chains that do not fit the experimental electron density. The EDS service also reported a negative bulk-solvent contribution B
factor and a negligibly small bulk-solvent contribution scale factor, which is abnormal for an experimentally determined protein structure (Fokine & Urzhumtsev, 2002
). Given the fact that the R
values calculated by PDB_REDO
from the data without refinement (0.265, 0.275; a new R
set was calculated by PDB_REDO
) agreed reasonably well with the values reported in the PDB header (0.298, 0.273), an accidental swap of experimentally observed structure factors F
(obs) against the final calculated structure factors F
(calc) when generating the deposited structure-factor file can be excluded (in that case also the reproduced R
values without refinement would be improbably low). In view of these discrepancies it seemed sensible to re-examine the 3k78
model and the associated deposited diffraction data.
The crystal structure model of birch pollen hypoallergen Bet v 1d (Zaborsky et al.
), PDB code 3k78
, was reported as solved by molecular replacement (MR) from the nearly sequence identical model of the hypoallergenic isoform Bet v 1l (Marković-Housley et al.
), PDB entry 1fm4
. The model structures are isomorphous (P
) with cell constants identical within experimental error. 1fm4
itself was derived by MR from the C
structure model of the clinically important inhalant major allergen, Bet v 1a (Gajhede et al.
; PDB entry 1bv1
). A sequence alignment including additional information relevant to the following discussion is provided in Fig. 1.
Figure 1 Sequence alignment of Bet v 1 allergens. The yellow codes indicate sequence differences between search model 1fm4 and 3k78, while the red highlights indicate nine residues that contain zero occupancy atoms in both models, 1fm4 and 3k78 (more ...)
model was refined against structure factors with 2.8 Å resolution, and 1fm4
was refined at 2.0 Å. Both structures appear unremarkable (in a technical sense, no insult to biological relevance intended), and the refinement statistics and protocols reported in the PDB entries are appropriate for the resolution. However, on closer inspection, both the model and the structure-factor data of 3k78
exhibit highly unlikely, physically improbable (if not impossible) features. For reference, the results of the 3k78
analysis and re-refinement are compared with those obtained for the isomorphous 1fm4
structure of good and reproducible quality. This comparison may provide useful reference for the aspiring crystallographer and can serve as teaching material.