Catalytic Intermediate Crystal Structures of Cysteine Desulfurase from the Archaeon Thermococcus onnurineus NA1

Table 1

Data collection and refinement statistics.

Data collection	NAT/NAT (crystal I)	GD/GD (crystal II)	IAA/GD (crystal III)	PSF/PSF (crystal IV)
PDB accession code	5B7S	5B87	5B89	5B7U
X-ray source	PAL7A	PAL5C	PAL5C	PAL5C
Space group	P212121	P212121	P212121	P212121
Unit-cell parameters a, b, c (Å)	67.0, 92.5, 145.4	67.1, 93.6, 145.0	62.9, 78.7, 171.9	62.8, 78.5, 171.3
Resolution range (Å)	50.0–2.6	50.0–2.3	50.0–1.5	50.0–1.9
Number of observed reflections (unique)	198,476 (28,968)	261,138 (40,955)	1,605,206 (128,579)	635,661 (66,011)
Completeness (%)	99.9 (100)	96.0 (100)	94.1 (91.9)	97.0 (91.9)
Rmerge (%)	11.9 (41.6)	9.5 (38.0)	8.9 (56.6)	6.2 (30.6)
Average I/σ (I)	29.1 (7.1)	44.6 (5.3)	62.9 (6.5)	52.9 (12.2)
Refinement
Resolution (Å)	36.4 (2.6)	49.4 (2.3)	49. 6 (1.5)	38.3 (1.9)
Number of reflection (Fobs > 0 σ (Fobs))
Working set	27,449	38,845	122,068	62,613
Free R set	1465	2040	6444	3326
R/Rfree (%)^c	19.3 (25.9)	17.7 (21.3)	16.7 (19.4)	16.5 (20.2)
Protein atom number	6270	6215	6256	6286
Ligand atom number
Alanine	0	12	12	0
PLP	0	30	30	0
Cysteine	0	0	0	7
Isopropanol	0	0	0	4
Glycerol	0	0	6	0
1,2-Ethanediol	0	0	4	0
Water molecules	0	137	545	259
RMSD bond lengths (Å)	0.013	0.029	0.027	0.020
RMSD bond angles(^o)	1.676	2.776	2.418	1.889
Mean B factors (Å^2)
Main-chain atoms	50.9	39.9	17.1	21.0
Side-chain atoms	56.2	46.4	22.3	26.6
Ligand
Alanine	n.a.	51.8	32.1	n.a.
PLP	n.a.	32.5	22.9	n.a.
Cysteine	n.a.	n.a.	n.a.	46.6
Isopropanol	n.a.	n.a.	n.a.	36.7
Water atoms	n.a.	42.7	34.0	30.6
Glycerol	n.a.	n.a.	23.9	n.a.
1,2-Ethanediol	n.a.	n.a.	31.6	n.a.
Ramachandran plot (%)
Favored regions	96.0	96.5	97.7	97.1
Allowed regions	2.9	2.8	1.8	2.4
Outlier regions	1.1	0.7	0.5	0.5

Values in parentheses are for the highest resolution shell. NAT represents the native structure, GD the gem-diamine structure, IAA the internal aldimine structure with a product alanine, and PSF the persulfide-bound structure. , where is the mean intensity of ith observation of symmetry-related reflections hkl. I/σ (I) represents a signal to noise of reflections. where is the calculated protein structure factor from the atomic model ( was calculated with randomly selected 5% of the reflections). was calculated with the remaining 95% of the reflections in the same equation of . RMSD represents root-mean-square deviation. n.a.: not available.