6T0I | pdb_00006t0i

The wild type glucuronoyl esterase OtCE15A from Opitutus terrae in complex with the aldotetrauronic acid XUX

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GS0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution E8: 0.12 M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), 0.1 M Buffer System 2 pH 7.5 (Sodium HEPES; MOPS), and 50 % v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.406	α = 75.8
b = 44.173	β = 65.489
c = 50.237	γ = 70.984

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 EIGER X 4M		2018-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.53	32.49	88.56	0.04434	0.05191	0.02683	0.999	15.38	3.7		42551			22.42

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.53	1.59	67.55		1.33	0.8103	0.508	0.72	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6gs0	1.53	32.49	1.96	42107	4168	88.4	0.1638	0.1602	0.16	0.1955	0.19	30.33

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	21.2906
f_angle_d	1.1592
f_chiral_restr	0.063
f_bond_d	0.0103
f_plane_restr	0.0079

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3068
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	114

Software

Software
Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHENIX	phasing
PHENIX	refinement

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.