PDB-7xyr: Cystal Structure of Beta-glucuronidase from Bacteroides thetaiota...

ID or keywords:

Entry

Database: PDB / ID: 7xyr

Title

Cystal Structure of Beta-glucuronidase from Bacteroides thetaiotaomicron

Components

Beta-glucuronidase

Keywords

HYDROLASE / beta-glucuronidase

Function / homology

Function and homology information

hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 2 Å

Authors

Teng, X. / Wang, C.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Cystal Structure of Beta-glucuronidase from Bacteroides thetaiotaomicron
Authors: Teng, X. / Wang, C.

History

Deposition	Jun 2, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7xyr.cif.gz	142.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7xyr.ent.gz	103 KB	Display	PDB format
PDBx/mmJSON format	7xyr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7xyr_validation.pdf.gz	439.1 KB	Display	wwPDB validaton report
Full document	7xyr_full_validation.pdf.gz	442.4 KB	Display
Data in XML	7xyr_validation.xml.gz	26 KB	Display
Data in CIF	7xyr_validation.cif.gz	39.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xy/7xyr ftp://data.pdbj.org/pub/pdb/validation_reports/xy/7xyr	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (7) #39 - Mar 2003 lac Repressor similarity (7)

Deposited unit

A: Beta-glucuronidase

hetero molecules

68.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	101.582, 122.249, 105.122
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-971- HOH
2	1	A-1024- HOH
3	1	A-1145- HOH
4	1	A-1151- HOH

#1: Protein	Beta-glucuronidase Mass: 67340.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: GAN91_07525, GAO00_01885 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I0TE21, beta-glucuronidase
#2: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.67 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 10%PEG3350, 0.2 M NaCl,0.1 M MES PH 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 2 Å
Detector	Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 9, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 2 Å / Relative weight: 1
Reflection	Resolution: 2→23.892 Å / Num. obs: 44460 / % possible obs: 99.57 % / Redundancy: 2 % / CC_1/2: 0.997 / Net I/σ(I): 12.71
Reflection shell	Resolution: 2→2.071 Å / Num. unique obs: 4387 / CC_1/2: 0.866

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
CrysalisPro		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 2→23.892 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.929 / WR_factor R_free: 0.21 / WR_factor R_work: 0.172 / SU B: 4.755 / SU ML: 0.127 / Average fsc free: 0.9045 / Average fsc work: 0.9191 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2322	2260	5.1 %
R_work	0.1902	42053	-
all	0.192	-	-
obs	-	44313	99.573 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 24.639 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.002 Å²	-0 Å²	0 Å²
2-	-	-0.005 Å²	-0 Å²
3-	-	-	0.007 Å²

Refinement step

Cycle: LAST / Resolution: 2→23.892 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4383	0	37	452	4872

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	4511
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	4039
X-RAY DIFFRACTION	r_angle_refined_deg	1.502	1.643	6133
X-RAY DIFFRACTION	r_angle_other_deg	1.399	1.573	9405
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.815	5	543
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.801	23.096	239
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.445	15	734
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.434	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	590
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5035
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	967
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	906
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.208	0.2	4011
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	2128
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1898
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.189	0.2	363
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.139	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.228	0.2	38
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.136	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	1.958	2.464	2181
X-RAY DIFFRACTION	r_mcbond_other	1.951	2.462	2180
X-RAY DIFFRACTION	r_mcangle_it	2.854	3.678	2721
X-RAY DIFFRACTION	r_mcangle_other	2.853	3.68	2722
X-RAY DIFFRACTION	r_scbond_it	2.367	2.669	2330
X-RAY DIFFRACTION	r_scbond_other	2.366	2.669	2331
X-RAY DIFFRACTION	r_scangle_it	3.564	3.909	3412
X-RAY DIFFRACTION	r_scangle_other	3.563	3.91	3413
X-RAY DIFFRACTION	r_lrange_it	5.532	29.623	5260
X-RAY DIFFRACTION	r_lrange_other	5.532	29.625	5261

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.052	0.311	184	0.269	3073	X-RAY DIFFRACTION	99.6329
2.052-2.108	0.293	169	0.251	2988	X-RAY DIFFRACTION	99.8419
2.108-2.169	0.31	157	0.239	2920	X-RAY DIFFRACTION	99.9026
2.169-2.236	0.262	146	0.226	2854	X-RAY DIFFRACTION	99.6678
2.236-2.309	0.278	161	0.21	2737	X-RAY DIFFRACTION	99.7934
2.309-2.39	0.251	139	0.206	2673	X-RAY DIFFRACTION	99.6456
2.39-2.48	0.234	147	0.204	2568	X-RAY DIFFRACTION	99.5965
2.48-2.581	0.275	116	0.212	2468	X-RAY DIFFRACTION	99.3464
2.581-2.696	0.277	113	0.199	2384	X-RAY DIFFRACTION	99.2448
2.696-2.828	0.238	126	0.18	2274	X-RAY DIFFRACTION	99.2556
2.828-2.98	0.254	98	0.184	2171	X-RAY DIFFRACTION	99.2129
2.98-3.161	0.232	116	0.192	2057	X-RAY DIFFRACTION	99.4508
3.161-3.379	0.229	97	0.188	1946	X-RAY DIFFRACTION	99.9022
3.379-3.649	0.231	81	0.185	1836	X-RAY DIFFRACTION	99.8438
3.649-3.996	0.193	92	0.168	1666	X-RAY DIFFRACTION	100
3.996-4.466	0.191	79	0.142	1527	X-RAY DIFFRACTION	99.9378
4.466-5.154	0.144	84	0.136	1343	X-RAY DIFFRACTION	99.7902
5.154-6.306	0.185	79	0.168	1138	X-RAY DIFFRACTION	99.9179
6.306-8.889	0.252	55	0.19	918	X-RAY DIFFRACTION	100
8-10	0.23	21	0.198	512	X-RAY DIFFRACTION	93.1818

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