9HUC | pdb_00009huc

The glucuronyl esterase OtCE15A from Opitutus terrae in complex with a heptasaccharide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6T0I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	OtCE15A mixed 3:1 with reservoir containing 0.10 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1 M Buffer system 1, pH 6.5 (Imidazole; MES monohydrate (acid)), 37.50 % v/v, Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350). Solid oligosaccharide added to the drop and soaked for 15 min.

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.77	α = 90
b = 65.43	β = 90
c = 118.62	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 6M		2022-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.03285	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.4	38.6	92.3	0.184	0.993	11.15	4.567		14772

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.47	78		0.718	0.786	2.42	3.59

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.403	38.599	14772	761	92.244	0.172	0.1676	0.1753	0.2451	0.2553	35.295

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]
-1.981			2.421		-0.441

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.781
r_dihedral_angle_6_deg	15.305
r_dihedral_angle_1_deg	7.092
r_dihedral_angle_2_deg	6.174
r_lrange_other	5.843
r_lrange_it	5.84
r_scangle_it	4.249
r_scangle_other	4.249
r_mcangle_other	3.417
r_mcangle_it	3.413
r_scbond_it	2.627
r_scbond_other	2.626
r_mcbond_it	2.171
r_mcbond_other	2.17
r_angle_refined_deg	1.343
r_angle_other_deg	0.473
r_symmetry_nbd_other	0.211
r_nbd_refined	0.21
r_nbtor_refined	0.179
r_nbd_other	0.17
r_metal_ion_refined	0.162
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.104
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.069
r_symmetry_nbd_refined	0.047
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3055
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	69

Software

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