7B7H | pdb_00007b7h

The glucuronoyl esterase OtCE15A R268A variant from Opitutus terrae in complex with, and covalently linked to, D-glucuronate

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	6.5	298	Morpheus screen consisting of 0.1 M buffer system 1 (imidazole and MES), 30% precipitant mix 2 (ethylene glycol and PEG 8000) and amino acid additives (L-Glutamate, Alanine (racemic); Glycine; Lysine HCl (racemic); Serine (racemic)). Soaking was carried out in a saturated solution of Bnz-GlcA in 10% DMSO and 90% mother liquor for 30 seconds before being flash frozen.

Crystal Properties
Matthews coefficient	Solvent content
2	38.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.333	α = 61.947
b = 47.298	β = 67.92
c = 51.112	γ = 88.272

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 16M		2020-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	1.008	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.796	43.15	96.62	0.1202	0.995	6.84	3.6		32171			25.74

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.796	1.861	92.99		1.256	0.461	0.95	3.6

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	1.8	43.15	1.97	32152	1988	96.62	0.1851	0.1826	0.18	0.2224	0.22	32.54

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	14.3775
f_angle_d	0.897
f_chiral_restr	0.054
f_plane_restr	0.008
f_bond_d	0.0069

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2868
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	126

Software

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

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.