Table 1.
X-ray crystallographic data
| PAb apo | PAb product | PAb dTDPR | PAb dTDPX | MTb dTDPR | SSb dTDPR | |
|---|---|---|---|---|---|---|
| Wavelength (Å) | 1.54 | 0.933 | 0.87 | 0.87 | 1.488 | 0.87 |
| Resolution (Å) Highest Shell | 40.41-2.53 (2.67-2.53) | 20.59-1.7 (1.79-1.70) | 39.68-2.0 (2.11-2.0) | 43.44-1.8 (1.9-1.8) | 36.2-1.79 (1.89-1.79) | 43-1.6 (1.69-1.60) |
| Cell dimension |
a=b=57.8
c=161.6 |
a =64.4
b =146.2 c =44.9 |
a =64.9
b =125.5 c =109.4 |
a =64.8
b =148.1 c =45.4 |
a =44.8
b =56.8 c =90.7 α=89.9° β=82.3° γ=78.3° |
a =51.4
b =141.5 c =53.6 |
| Space group | P41212 | P21212 | C2221 | P21212 | P1 | P21 |
| Unique reflections | 9710 | 40067 | 30581 | 35190 | 84823 | 99569 |
| Average redundancy | 7.3 (6.3) | 6.1(4.7) | 4.0(4.0) | 3.0(3.1) | 2.2(2.2) | 4.9(4.1) |
| I/σ | 6.8(1.8) | 5.6(1.8) | 6.3(2.1) | 5.5(2.2) | 7.5(1.8) | 6.6(2.8) |
| Completeness (%) | 99.2(99.4) | 84.3(44.1) | 99.9(99.9) | 80.1(66.1) | 92.6(89.3) | 99.1(94.7) |
| Rmergea (%) | 8.8(41.9) | 8.6(38.4) | 8.4(35.6) | 9.6(34.9) | 6.5(29.9) | 7.0(24.8) |
| No of molecules in asymmetric unit | 1 | 2 | 2 | 2 | 4 | 4 |
| Refinement | ||||||
| R (%) | 20.0(31.9) | 15.0(17.4) | 19.0(24.5) | 18.6(21.7) | 15.2(18.3) | 16.7(17.8) |
| Rfree (5% of data) (%) | 27.8(44.7) | 19.8(25.3) | 25.6(29.2) | 23.7(28.8) | 19.6(25.9) | 21.2(27.4) |
| rmsd bonds (Å) / angles (º) | 0.014/1.4 | 0.011/1.4 | 0.008/1.12 | 0.009/1.6 | 0.012/1.3 | 0.012/1.3 |
| B-factor deviation bonds / angles (Å2): | ||||||
| main chain | 0.6/1.0 | 1.3/1.5 | 0.5/0.6 | 0.7/0.7 | 0.9/1.2 | 0.9/1.2 |
| side chains | 1.5/2.3 | 2.2/3.1 | 0.9/1.3 | 1.2/1.9 | 1.9/2.6 | 1.8/2.5 |
| Residues in Ramachandran Core (%) | 89 | 94 | 93 | 93 | 91 | 91 |
| Protein atoms | 1490 | 2982 | 2980 | 2992 | 6164 | 6335 |
| Water atoms | 92 | 531 | 590 | 455 | 1168 | 1383 |
| dTDP ligand atoms | 10 | 70 | 70 | 50 c | 140 | 140 |
| Protein average B-factor (Å2) | 26 | 15 | 35 | 20 | 26 | 12 |
| Average B-factor (Å2) of dTDP-ligand | N/A | 21 | 27 | 36c | 35 | 15 |
| Average B-factor (Å2) waters | 40 | 37 | 55 | 37 | 47 | 30 |
| PDB accession code | 2ixj | 2ixk | 2ixh | 2ixi | 2ixc | 2ixl |
a
Rmerge = ∑hkl ∑l|Ii − <I>|/∑hkl ∑l <I>, where Ii is an intensity for the ith measurement of a reflection with indices hkl and <I> is the weighted mean of the reflection intensity
b
PA P. aeruginosa, MT M. tuberculosis, SS S. suis. dTDPR:dTDP-L-rhamnose, dTDPX: dTDP-D-xylose, dTDPG: dTDP-D-glucose.
c
The carbohydrate portion of this ligand is partly disordered.