Table 1.
Summary of Crystallography
| Crystal form | CurF ER (NADP+) | JamJ ER (free enzyme) | JamJ ER (NADPH) | Se-Met JamJ ER (NADPH) | CurK ER (free enzyme) |
|---|---|---|---|---|---|
| Diffraction data | |||||
| X ray source | APS 23ID-D | APS 23ID-D | APS 23ID-B | APS 23ID-D | APS 23ID-B |
| Wavelength (Å) | 0.72932 | 1.0332 | 1.0332 | 0.979 | 1.0332 |
| Space group | C2 | P1 | P31 | P31 | F222 |
| Cell dimensions | |||||
| a, b, c (Å) | 108.9, 47.3, 76.9 | 50.9, 57.2, 66.1 | 110.7, 92.8 | 111.3, 91.6 | 93.6, 127.1, 127.8 |
| α, β, γ (°) | β=123.4 | 95.3, 106.7, 105.1 | |||
| dmin (Å) | 0.96 (1.01–0.96)* | 1.80 (1.86–1.80) | 2.25 (2.33–2.25) | 2.6 (2.69–2.60) | 1.85 (1.92–1.85) |
| Rmerge (%) | 8.0 (66.0) | 7.4 (70.2) | 7.3 (60.9) | 12.1 (60.5) | 5.9 (62.2) |
| Avg I/σI | 9.5 (1.5) | 14.2 (2.0) | 12.3 (1.4) | 25.8 (3.3) | 21.0 (1.9) |
| Observations (#) | 197,326 | 63,164 | 59,866 | 19,823 | 32,609 |
| Completeness (%) | 99.9 (94.2) | 95.2 (95.8) | 99.6 (99.8) | 100.0 (100.0) | 99.0 (100.0) |
| Avg multiplicity | 3.7 (2.7) | 2.2 (2.2) | 2.1 (2.0) | 5.7 (5.8) | 3.8 (3.7) |
| Refinement | |||||
| Data range (Å) | 23.0–0.96 | 46.5–1.8 | 45.6–2.25 | 24.3–1.85 | |
| Reflections (#) | 187,338 | 58,496 | 56,585 | 30,569 | |
| Rwork/Rfree (%) | 11.7/13.1 | 18.6/22.7 | 17.9/21.5 | 18.5/22.0 | |
| Number of atoms | |||||
| Protein | 2843 | 5320 | 8064 | 2619 | |
| Water | 558 | 414 | 362 | 230 | |
| Ligands | 48 | – | 141 | – | |
| RMS deviations | |||||
| Bond lengths (Å) | 0.01 | 0.010 | 0.005 | 0.008 | |
| Bond angles (°) | 1.529 | 1.35 | 1.048 | 1.15 | |
| Avg B-factors (Å2) Protein NADP Water |
10.3 8.3 30.9 |
31 – 41 |
39.5 29.3 32.6 |
35.4 – 46.5 |
|
| MolProbity score | 1.1 | 1.23 | 1.32 | 1.18 | |
| MolProbity clashscore | 3.06 | 4.55 | 3.66 | 3.94 | |
| Ramachandran plot | |||||
| Favored (%) | 98.92 | 98.07 | 95.96 | 98.8 | |
| Allowed (%) | 1.08 | 1.1 | 3.74 | 0.9 | |
| Outliers (%) | 0.0 | 0 | 0.3 | 0.3 | |
| Molecular state | |||||
| Asymmetric unit | 1 monomer | 2 monomers | 3 monomers | 1 monomer | |
| Active site ligands | NADP+ | – | NADPH | – | |
| PDB code | 5DP2 | 5DOV | 5DOZ | 5DP1 |
*
Values in parentheses are for the highest-resolution shell.