PDB-8z43: Beta-galactosidase from Bacteroides xylanisolvens (E350G, ligand-free)

ID or keywords:

Entry

Database: PDB / ID: 8z43

Title

Beta-galactosidase from Bacteroides xylanisolvens (E350G, ligand-free)

Components

Beta-galactosidase

Keywords

HYDROLASE / glycoside hydrolase

Function / homology

Domain of unknown function DUF5597 / Domain of unknown function (DUF5597) / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / Beta-galactosidase

Function and homology information

Biological species

Bacteroides xylanisolvens XB1A (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.91 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

-
Download

PDBx/mmCIF format	8z43.cif.gz	238.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8z43.ent.gz	182.2 KB	Display	PDB format
PDBx/mmJSON format	8z43.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8z43_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8z43_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8z43_validation.xml.gz	47.9 KB	Display
Data in CIF	8z43_validation.cif.gz	66.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z4/8z43 ftp://data.pdbj.org/pub/pdb/validation_reports/z4/8z43	HTTPS FTP

-
Related structure data

Related structure data	8z47C 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-galactosidase

B: Beta-galactosidase

hetero molecules

125 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-galactosidase

B: Beta-galactosidase

hetero molecules

A: Beta-galactosidase

B: Beta-galactosidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	144.699, 51.062, 180.085
Angle α, β, γ (deg.)	90.000, 90.415, 90.000
Int Tables number	5
Space group name H-M	I121

#1: Protein	Beta-galactosidase Mass: 62524.422 Da / Num. of mol.: 2 / Mutation: E350G 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: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: sodium citrate tribasic dihydrate, PEG 3350, bis-Tris propane

-
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: Dec 10, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.91→48.198 Å / Num. obs: 102654 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC_1/2: 0.999 / Net I/σ(I): 15.8
Reflection shell	Resolution: 1.91→1.94 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5058 / CC_1/2: 0.754

-
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: 1.91→48.152 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.95 / SU B: 3.305 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.202	5220	5.085 %
R_work	0.1742	97427	-
all	0.176	-	-
obs	-	102647	99.843 %

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: 27.594 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0 Å²	0 Å²
2-	-	-0.023 Å²	-0 Å²
3-	-	-	0.003 Å²

Refinement step

Cycle: LAST / Resolution: 1.91→48.152 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8428	0	12	528	8968

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	8702
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8036
X-RAY DIFFRACTION	r_angle_refined_deg	1.682	1.809	11818
X-RAY DIFFRACTION	r_angle_other_deg	0.588	1.758	18532
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.15	5	1056
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.304	5	32
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.8	10	1434
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.125	10	402
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	1254
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	10270
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2062
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	1638
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	7389
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	4266
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	4433
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	499
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.027	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.249	0.2	68
X-RAY DIFFRACTION	r_nbd_other	0.2	0.2	169
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.155	0.2	51
X-RAY DIFFRACTION	r_mcbond_it	2.348	2.708	4230
X-RAY DIFFRACTION	r_mcbond_other	2.347	2.708	4230
X-RAY DIFFRACTION	r_mcangle_it	3.154	4.851	5284
X-RAY DIFFRACTION	r_mcangle_other	3.154	4.851	5285
X-RAY DIFFRACTION	r_scbond_it	3.403	3.053	4472
X-RAY DIFFRACTION	r_scbond_other	3.403	3.053	4473
X-RAY DIFFRACTION	r_scangle_it	5.097	5.431	6534
X-RAY DIFFRACTION	r_scangle_other	5.097	5.431	6535
X-RAY DIFFRACTION	r_lrange_it	6.153	30.235	9978
X-RAY DIFFRACTION	r_lrange_other	6.153	30.234	9979

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
1.91-1.96	0.289	367	0.253	7200	0.255	7568	0.943	0.954	99.9868	0.218
1.96-2.013	0.29	322	0.24	6997	0.242	7323	0.942	0.96	99.9454	0.203
2.013-2.071	0.233	383	0.21	6777	0.211	7161	0.963	0.97	99.986	0.173
2.071-2.135	0.243	320	0.207	6615	0.209	6938	0.959	0.971	99.9568	0.171
2.135-2.205	0.224	341	0.191	6377	0.192	6719	0.969	0.976	99.9851	0.156
2.205-2.282	0.246	319	0.186	6180	0.189	6499	0.961	0.977	100	0.152
2.282-2.368	0.228	396	0.181	5910	0.184	6310	0.968	0.979	99.9366	0.148
2.368-2.465	0.214	281	0.169	5772	0.171	6058	0.972	0.982	99.9175	0.137
2.465-2.574	0.224	292	0.17	5545	0.173	5840	0.97	0.982	99.9486	0.142
2.574-2.699	0.181	293	0.157	5278	0.158	5571	0.98	0.984	100	0.131
2.699-2.845	0.219	248	0.169	5035	0.172	5285	0.966	0.981	99.9622	0.145
2.845-3.016	0.218	274	0.172	4762	0.175	5042	0.968	0.981	99.881	0.148
3.016-3.224	0.188	194	0.166	4521	0.167	4725	0.979	0.982	99.7884	0.148
3.224-3.481	0.201	201	0.171	4192	0.172	4411	0.971	0.982	99.5919	0.157
3.481-3.811	0.198	240	0.17	3813	0.171	4066	0.976	0.983	99.6803	0.16
3.811-4.258	0.172	208	0.153	3486	0.154	3712	0.983	0.986	99.5151	0.147
4.258-4.91	0.157	204	0.14	3054	0.141	3270	0.984	0.988	99.633	0.138
4.91-5.998	0.188	150	0.168	2610	0.169	2786	0.984	0.986	99.0668	0.166
5.998-8.417	0.184	116	0.182	2090	0.182	2219	0.982	0.98	99.4142	0.179
8.417-48.152	0.148	71	0.168	1213	0.167	1296	0.988	0.982	99.0741	0.173

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi