PDB-8z47: Beta-galactosidase from Bacteroides xylanisolvens (ligand-free)

ID or keywords:

Entry

Database: PDB / ID: 8z47

Title

Beta-galactosidase from Bacteroides xylanisolvens (ligand-free)

Components

Beta-galactosidase

Keywords

HYDROLASE / glycoside hydrolase

Function / homology

Function and homology information

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

Biological species

Bacteroides xylanisolvens XB1A (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.86 Å

Authors

Nakajima, M. / Motouchi, S. / Kobayashi, K.

Funding support

1items

Citation

Journal: Commun Biol / Year: 2025
Title: Structure and function of a beta-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium.
Authors: Nakazawa, Y. / Kageyama, M. / Matsuzawa, T. / Liang, Z. / Kobayashi, K. / Shimizu, H. / Maeda, K. / Masuhiro, M. / Motouchi, S. / Kumano, S. / Tanaka, N. / Kuramochi, K. / Nakai, H. / Taguchi, H. / Nakajima, M.

History

Deposition	Apr 16, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 1, 2025	Provider: repository / Type: Initial release
Revision 1.1	Mar 19, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8z47.cif.gz	124.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8z47.ent.gz	89.6 KB	Display	PDB format
PDBx/mmJSON format	8z47.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8z47_validation.pdf.gz	787.5 KB	Display	wwPDB validaton report
Full document	8z47_full_validation.pdf.gz	788.6 KB	Display
Data in XML	8z47_validation.xml.gz	23.7 KB	Display
Data in CIF	8z47_validation.cif.gz	33 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z4/8z47 ftp://data.pdbj.org/pub/pdb/validation_reports/z4/8z47	HTTPS FTP

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Related structure data

Related structure data	8z43C 8z48C C: citing same article (ref.)
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

Deposited unit

A: Beta-galactosidase

hetero molecules

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

1

A: Beta-galactosidase

hetero molecules

A: Beta-galactosidase

hetero molecules

A: Beta-galactosidase

hetero molecules

A: Beta-galactosidase

hetero molecules

defined by author
Evidence: Homotetramer according to PISA analysis
251 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	163.831, 163.831, 50.857
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4

#1: Protein

Beta-galactosidase

Mass: 62596.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacteroides xylanisolvens XB1A (bacteria)
Gene: BXY_22780 / Production host:

Escherichia coli (E. coli) / References: UniProt: D6CYU7

#2: Sugar

ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

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: 2.73 Å³/Da / Density % sol: 54.88 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: potassium thiocyanate, PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.86→41.78 Å / Num. obs: 57035 / % possible obs: 100 % / Redundancy: 6.6 % / CC_1/2: 0.996 / Net I/σ(I): 10.3
Reflection shell	Resolution: 1.86→1.9 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3503 / CC_1/2: 0.711

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.86→41.779 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.946 / WR_factor R_free: 0.231 / WR_factor R_work: 0.196 / Average fsc free: 0.9603 / Average fsc work: 0.971 / Cross valid method: FREE R-VALUE / ESU R: 0.123 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2265	2889	5.066 %
R_work	0.1925	54141	-
all	0.194	-	-
obs	-	57030	99.928 %

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: 32.324 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	-0 Å²	-0 Å²
2-	-	0 Å²	-0 Å²
3-	-	-	-0 Å²

Refinement step

Cycle: LAST / Resolution: 1.86→41.779 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4015	0	12	223	4250

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	4135
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	3842
X-RAY DIFFRACTION	r_angle_refined_deg	1.684	1.813	5613
X-RAY DIFFRACTION	r_angle_other_deg	0.905	1.761	8864
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.953	5	501
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	17.239	5	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.338	10	690
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.271	10	189
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	601
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	4857
X-RAY DIFFRACTION	r_gen_planes_other	0.012	0.02	967
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	792
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.208	0.2	3453
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	2035
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	2061
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	203
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.008	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.1	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.189	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.147	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	2.831	3.157	2010
X-RAY DIFFRACTION	r_mcbond_other	2.831	3.157	2010
X-RAY DIFFRACTION	r_mcangle_it	3.705	5.665	2509
X-RAY DIFFRACTION	r_mcangle_other	3.705	5.666	2510
X-RAY DIFFRACTION	r_scbond_it	3.827	3.54	2125
X-RAY DIFFRACTION	r_scbond_other	3.826	3.54	2126
X-RAY DIFFRACTION	r_scangle_it	5.604	6.311	3104
X-RAY DIFFRACTION	r_scangle_other	5.603	6.311	3105
X-RAY DIFFRACTION	r_lrange_it	6.749	34.039	4719
X-RAY DIFFRACTION	r_lrange_other	6.748	34.038	4720

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.86-1.908	0.307	196	0.276	3984	0.277	4182	0.934	0.946	99.9522	0.257
1.908-1.96	0.29	220	0.256	3853	0.257	4074	0.946	0.955	99.9755	0.236
1.96-2.017	0.284	183	0.246	3791	0.248	3974	0.942	0.96	100	0.225
2.017-2.079	0.248	200	0.219	3641	0.22	3841	0.962	0.969	100	0.198
2.079-2.147	0.275	178	0.217	3561	0.219	3739	0.947	0.969	100	0.196
2.147-2.222	0.24	170	0.208	3426	0.209	3596	0.964	0.972	100	0.189
2.222-2.306	0.272	205	0.198	3324	0.202	3529	0.958	0.974	100	0.181
2.306-2.4	0.226	188	0.197	3162	0.199	3352	0.967	0.976	99.9403	0.181
2.4-2.506	0.251	159	0.202	3068	0.204	3229	0.961	0.974	99.9381	0.189
2.506-2.628	0.251	153	0.199	2926	0.201	3079	0.965	0.977	100	0.187
2.628-2.769	0.251	125	0.197	2834	0.199	2960	0.961	0.977	99.9662	0.189
2.769-2.937	0.215	148	0.193	2632	0.194	2781	0.972	0.977	99.964	0.19
2.937-3.138	0.234	124	0.192	2509	0.194	2634	0.967	0.977	99.962	0.195
3.138-3.388	0.22	159	0.195	2312	0.197	2473	0.971	0.977	99.9191	0.203
3.388-3.709	0.231	104	0.188	2131	0.19	2235	0.968	0.979	100	0.201
3.709-4.143	0.194	111	0.17	1936	0.171	2048	0.979	0.983	99.9512	0.191
4.143-4.776	0.197	95	0.156	1719	0.158	1823	0.979	0.986	99.5063	0.184
4.776-5.83	0.193	71	0.171	1486	0.172	1559	0.979	0.983	99.8717	0.2
5.83-8.166	0.24	56	0.188	1171	0.19	1227	0.971	0.979	100	0.213
8.166-41.779	0.155	44	0.174	675	0.172	730	0.981	0.98	98.4932	0.203

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