Alternative models for two crystal structures of Candida albicans 3,4-dihydroxy-2-butanone 4-phosphate synthase
✍ Scribed by Le Trong, Isolde ;Stenkamp, Ronald E.
- Publisher
- International Union of Crystallography
- Year
- 2008
- Tongue
- English
- Weight
- 68 KB
- Volume
- 64
- Category
- Article
- ISSN
- 0907-4449
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✦ Synopsis
Reinterpretation of the space-group symmetry is reported for two crystal structures of Candida albicans 3,4-dihydroxy-2-butanone 4-phosphate synthase (PDB codes 1tks and 1tku). The two structures reported in space group P1 with a dimer in the asymmetric unit can be described as C-centered monoclinic structures with one subunit in the asymmetric unit.
Two crystal structures of 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBPS) from Candida albicans have been deposited in the Protein Data Bank (Echt et al., 2004). PDB entry 1tks contains a model for the unliganded enzyme, while PDB entry 1tku is a d-ribulose 5-phosphate (Ru5P) complex of the protein. The structures are isomorphous (see Table 1) and were solved in space group P1 with two identical polypeptide chains in the asymmetric unit. The authors reported the presence of a noncrystallographic twofold rotation axis that relates the two chains in what is believed to be the physiologically important dimer.
We re-examined these structures after surveying WHAT_CHECK results (Hooft et al., 1996) for PDB entries with more than one molecule in the asymmetric unit. The small r.m.s. deviations from an average structure for the two molecules in the asymmetric unit attracted our attention, as did the nearly 90 angles for the two triclinic unit cells.
Visual inspection shows that the dyad relating the two subunits is collinear with the b axis of the triclinic unit cell and applies to the entire crystal. Thus, the crystal structures possess monoclinic symmetry. This is also seen in the deposited diffraction data.
An alternate description of the crystal structures is possible in space group C2 with a single subunit in the asymmetric unit. The transformation used to convert the reflection indices to the monoclinic cell was h monoclinic = Àk triclinic + 2l triclinic , k monoclinic = Àk triclinic , l monoclinic = h triclinic . Averaging of the replicate measurements related by the 2/m monoclinic symmetry resulted in R merge values of 0.034 and 0.024 for the diffraction data for PDB entries 1tks and 1tku, respectively. The number of unique reflections was reduced from 43 263 to 24 177 for the free enzyme and from 39 344 to 20 361 for the Ru5P complex. The triclinic data sets were reported as being 84.4% and 77.3% complete (Echt et al., 2004). (We have been unable to confirm the 77.3% value owing to an inconsistency between the reported number of reflections and the resolution limits for the Ru5P complex.) The reindexed monoclinic sets were 91.9% and 93.0% complete for the enzyme and Ru5P complex, respectively. Table 1 contains a comparison of the triclinic and monoclinic unit-cell parameters.
An initial model was oriented and positioned in the monoclinic cell with MOLREP (Collaborative Computational Project, Number 4, 1994) using the A chain of 1tks as the probe. Water molecules from 1tks were added to the model if they were within 4 A ˚of atoms in the A chain, if they had a matching water molecule bound to the B chain and if they were located in a peak higher than 1 in a difference electron-density map calculated for the MOLREP solution. A refined model for the free enzyme served as the initial model for the Ru5P complex. Superposition of the A chain of 1tku, along with its waters