6UB1 | pdb_00006ub1

Crystal structure of a GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii (BgGH128_III) in complex with laminaribiose at -3 and -2 subsites

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6UAY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.05 M Potassium di-hydrogen phosphate, 24% Polyethylene glycol 8,000

Crystal Properties
Matthews coefficient	Solvent content
1.76	30.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.323	α = 69.67
b = 60.804	β = 78.24
c = 63.545	γ = 77.86

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2017-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.458540	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.6	35.49	86.2	0.994	13.35	3.3		87019

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.7	86.8		0.986	7.48	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6UAY	1.6	35.49	82649	4350	86.27	0.1623	0.1604	0.1969	RANDOM	16.249

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-1.11	-0.25	-0.27	0.68	-0.32	-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.126
r_dihedral_angle_4_deg	18.668
r_dihedral_angle_1_deg	18.229
r_dihedral_angle_3_deg	12.832
r_angle_refined_deg	1.945
r_angle_other_deg	1.599
r_chiral_restr	0.106
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.126
r_dihedral_angle_4_deg	18.668
r_dihedral_angle_1_deg	18.229
r_dihedral_angle_3_deg	12.832
r_angle_refined_deg	1.945
r_angle_other_deg	1.599
r_chiral_restr	0.106
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6988
Nucleic Acid Atoms
Solvent Atoms	1096
Heterogen Atoms	81

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.