Archaea

Research Article

NADP-Dependent Aldehyde Dehydrogenase from Archaeon Pyrobaculum sp.1860: Structural and Functional Features

Data collection and refinement statistics. Values in parentheses are for the highest resolution shell.


	Apo	Holo-1	Holo-2	Holo-3	Ternary complex

PDB entry	5EEB	5F2C	5EUY	5EXF	5EK6
Data collection
Space group	P 2₁ 2₁ 2	P 2₁ 2₁ 2	P 2₁ 2₁ 2	P 2₁ 2₁ 2	P 2₁ 2₁ 2
Cell dimensions
(Å)	184.24	185.36	184.77	185.59	183.80
(Å)	207.23	208.30	208.05	208.72	207.85
(Å)	164.96	163.81	165.40	164.75	166.44
Temperature (K)	100	100	100	100	100
Wavelength (Å)	0.984	0.800	0.970	1.00	0.972
Crystal-to-detector distance (mm)	168.0	300.0	363.1	300.0	386.9
Oscillation range (°)	1.0	0.5	0.1	0.5	0.1
Number of frames	197	720	1120	720	1450
Resolution (°)	29.77–3.04	29.15–1.90	59.06–2.06	90.97–2.19	59.14–2.66
Completeness (%)	98.9 (85.0)	99.8 (99.0)	99.1 (99.0)	98.2 (97.9)	99.34 (100)
R-merge	0.27 (0.76)	0.07 (0.33)	0.10 (0.77)	0.19 (0.73)	0.17 (0.77)
I/	7.7 (2.3)	13.4 (1.6)	8.3 (1.6)	5.3 (1.7)	7.3 (1.8)
Redundancy	7.4	4.0	4.1	4.9	5.4
Refinement
/	0.202/0.256	0.184/0.218	0.196/0.233	0.206/0.245	0.189/0.240
Wilson B-factor (Å²)	43.5	25.0	35.3	22.0	42.0
Number of atoms
All	30043	34276	33663	33881	30912
(i) Protein	30043	30690	30355	30382	30054
(ii) NADP+	—	396	408	384	384
(iii) Isobut.	—	—	—	—	30
(iv) Glycerol	—	6	—	6	—
(v) Water molecules	—	3184	2900	3109	444
Average B, all atoms (Å²)	35.0	28.0	37.0	27.0	40.0
RMS deviations
(i) Bond lengths	0.010	0.008	0.008	0.008	0.011
(ii) Bond angles	1.274	1.021	1.058	1.071	1.197
Ramachandran plot
Most favorable (%)	97.43	97.34	96.80	96.24	95.41
Allowed (%)	2.47	2.45	2.86	3.40	3.94
Outliers (%)	0.1	0.21	0.34	0.37	0.65