Crystal structure and functional characterization of an oligosaccharide dehydrogenase from Pycnoporus cinnabarinus provides insights into fungal breakdown of lignocellulose

Table 2 X-ray diffraction data collection and structure refinement statistics. Values in parentheses are for the highest-resolution shell

	Ligand-free ODH 6XUT	ODH-GLC 6XUU	ODH-G3G 6XUV
Data collection
Space group	P2₁2₁2₁
Unit-cell dimensions (Å)	a = 48.87 b = 61.59 c = 195.09
Resolution range (Å)	97.55–1.43 (1.57–1.43)	49.04–1.57 (1.67–1.57)	97.33–1.75 (2.02–1.75)
Number of observations	1,391,283 (295,026)	1,064,709 (190,424)	770,177 (268,996)
Unique reflections	128,942 (25,836)	103,996 (29,033)	59,350 (20,470)
Completeness (%)	99.9 (99.7)	99.6 (98.8)	99.9 (99.8)
Redundancy	12.7 (11.4)	6.6 (6.6)	13.0 (13.1)
I/σ(I)	14.5 (1.72)	12.0 (1.36)	7.0 (1.97)
R_merge^a (%)	7.1 (139.0)	9.0 (141.0)	17.5 (156.1)
CC_1/2	100 (79.5)	99.9 (55.8)	99.9 (80.8)
Wilson B-value (Å²)	22.0	28.6	25.9
Refinement
Resolution range (Å)	97.55–1.60	49.04–1.57	97.33–1.75
Protein molecules per asymmetric unit	1	1	1
R_work/R_free^b	0.165/0.196	0.162/0.189	0.168/0.207
Deviations from ideal geometry
Bond (Å)	0.0132	0.0127	0.0138
Angles (Å)	1.713	1.856	2.005
Ramachandran plot (%) Favored/allowed/outliers	95.4/4.6/0	96.25/3.75/0	96.25/3.75/0
Mean B-factors (Å²)
Protein	42.2	36.9	48.7
FAD/GLC/G3G	33.4/-/-	28.8/47.7/-	40.1/-/61.7
Water/sulfate	41.8/55.9	42.7/85.9	52.6/105.3
Number of atoms
Protein	5023	4902	5059
FAD/GLC/G3G	53/-/-	53/108/-	53/-/115
Water/sulfate	466/40	363/20	303/15

^a\(R_{{{\text{merge}}}} = \mathop \sum \limits_{i} \mathop \sum \limits_{j} |~I_{{i,j}} - I_{j} |/\mathop \sum \limits_{i} \mathop \sum \limits_{j} I_{{i,j}}\), where i runs over multiple observations of the same intensity, and j runs over all crystallographically unique intensities.
^b\(R_{{{\text{work}}}} = \sum \left| {\left| {F_{{{\text{obs}}}} } \right| - \left| {F_{{{\text{calc}}}} } \right|} \right|~/~\sum \left| {F_{{{\text{obs}}}} } \right|/\mathop \sum \limits_{i} \mathop \sum \limits_{j} I_{{i,j}}\), where |F_obs|> 0. R_free is based on 5% of the data randomly selected and is not used in the refinement.

ISSN: 2731-3654