PDB-8h25: Lacticaseibacillus casei GH35 beta-galactosidase LBCZ_0230

ID or keywords:

Entry

Database: PDB / ID: 8h25

Title

Lacticaseibacillus casei GH35 beta-galactosidase LBCZ_0230

Components

Beta-galactosidase

Keywords

HYDROLASE / beta-galactosidase / GH35 / lacto-N-biose 1 / galacto-N-biose

Function / homology

Function and homology information

beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function

Biological species

Lacticaseibacillus casei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.295 Å

Authors

Saburi, W. / Ota, T. / Kato, K. / Tagami, T. / Yamashita, K. / Yao, M. / Mori, H.

Funding support

1items

Citation

Journal: J Appl Glycosci (1999) / Year: 2023
Title: Function and Structure of Lacticaseibacillus casei GH35 beta-Galactosidase LBCZ_0230 with High Hydrolytic Activity to Lacto- N -biose I and Galacto- N -biose.
Authors: Saburi, W. / Ota, T. / Kato, K. / Tagami, T. / Yamashita, K. / Yao, M. / Mori, H.

History

Deposition	Oct 4, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 16, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8h25.cif.gz	489.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8h25.ent.gz	388.4 KB	Display	PDB format
PDBx/mmJSON format	8h25.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8h25_validation.pdf.gz	485 KB	Display	wwPDB validaton report
Full document	8h25_full_validation.pdf.gz	499.5 KB	Display
Data in XML	8h25_validation.xml.gz	80.5 KB	Display
Data in CIF	8h25_validation.cif.gz	110.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h2/8h25 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/8h25	HTTPS FTP

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Related structure data

Related structure data	4e8dS S: Starting model for refinement
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 (1)

Deposited unit

A: Beta-galactosidase

B: Beta-galactosidase

C: Beta-galactosidase

D: Beta-galactosidase

hetero molecules

277 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-galactosidase

C: Beta-galactosidase

hetero molecules

defined by author&software
Evidence: native gel electrophoresis
139 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Beta-galactosidase

D: Beta-galactosidase

hetero molecules

defined by author&software
138 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.384, 110.998, 120.337
Angle α, β, γ (deg.)	90.000, 90.015, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 593 / Label seq-ID: 2 - 593

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Beta-galactosidase Mass: 68849.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lacticaseibacillus casei (bacteria) / Gene: FEI12_08385 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5R8LFD3
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#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.: 368 / 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: 2.24 Å³/Da / Density % sol: 45.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES-NaOH buffer (pH 7.5), 10% (v/v) 2-propanol, and 200 g/L polyethylene glycol 4000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL44XU / Wavelength: 0.9 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.5121
pseudo-merohedral	2	2	-h,-k,l	2	0.4879

Reflection

Resolution: 2.29→45.9 Å / Num. obs: 108220 / % possible obs: 99.7 % / Redundancy: 3.79 % / CC_1/2: 0.998 / R_merge(I) obs: 0.085 / Net I/σ(I): 13.24

Reflection shell

Resolution: 2.29→2.43 Å / Mean I/σ(I) obs: 2.38 / Num. unique obs: 17244 / CC_1/2: 0.768

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4E8D

4e8d

Resolution: 2.295→45.9 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.931 / SU B: 4.982 / SU ML: 0.127 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.232	5374	4.966 %
R_work	0.1947	102845	-
all	0.197	-	-
obs	-	108219	99.618 %

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: 43.496 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	33.108 Å²	0 Å²	-16.524 Å²
2-	-	-10.218 Å²	-0 Å²
3-	-	-	-22.891 Å²

Refinement step

Cycle: LAST / Resolution: 2.295→45.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19016	0	108	368	19492

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	19710
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	17256
X-RAY DIFFRACTION	r_angle_refined_deg	0.886	1.654	26825
X-RAY DIFFRACTION	r_angle_other_deg	0.317	1.565	40259
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.584	5	2366
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.791	5	88
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.583	10	3033
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.503	10	1001
X-RAY DIFFRACTION	r_chiral_restr	0.045	0.2	2794
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	22502
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4078
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	3703
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	16331
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	9298
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	10002
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	576
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.037	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.181	0.2	35
X-RAY DIFFRACTION	r_nbd_other	0.223	0.2	107
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.128	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	2.219	4.48	9473
X-RAY DIFFRACTION	r_mcbond_other	2.219	4.48	9473
X-RAY DIFFRACTION	r_mcangle_it	3.319	6.716	11836
X-RAY DIFFRACTION	r_mcangle_other	3.319	6.717	11837
X-RAY DIFFRACTION	r_scbond_it	2.077	4.624	10237
X-RAY DIFFRACTION	r_scbond_other	2.076	4.623	10235
X-RAY DIFFRACTION	r_scangle_it	3.179	6.875	14989
X-RAY DIFFRACTION	r_scangle_other	3.179	6.875	14990
X-RAY DIFFRACTION	r_lrange_it	4.952	54.375	21437
X-RAY DIFFRACTION	r_lrange_other	4.944	54.303	21411
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.081	0.05	20169
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.051	0.05	20602
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.079	0.05	20220
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.078	0.05	20169
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.051	0.05	20633
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.079	0.05	20175

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08147	0.05011
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08147	0.05011
2	3	A	X-RAY DIFFRACTION	Local ncs	0.0514	0.05011
2	4	A	X-RAY DIFFRACTION	Local ncs	0.0514	0.05011
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07874	0.05011
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07874	0.05011
4	7	A	X-RAY DIFFRACTION	Local ncs	0.07816	0.05011
4	8	A	X-RAY DIFFRACTION	Local ncs	0.07816	0.05011
5	9	A	X-RAY DIFFRACTION	Local ncs	0.05109	0.05011
5	10	A	X-RAY DIFFRACTION	Local ncs	0.05109	0.05011
6	11	A	X-RAY DIFFRACTION	Local ncs	0.07919	0.05011
6	12	A	X-RAY DIFFRACTION	Local ncs	0.07919	0.05011

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 (%)
2.295-2.354	0.518	370	0.405	7360	X-RAY DIFFRACTION	96.7944
2.354-2.419	0.405	407	0.367	7422	X-RAY DIFFRACTION	99.9745
2.419-2.489	0.37	372	0.321	7206	X-RAY DIFFRACTION	99.9736
2.489-2.565	0.329	368	0.291	6979	X-RAY DIFFRACTION	100
2.565-2.649	0.321	363	0.245	6793	X-RAY DIFFRACTION	99.9162
2.649-2.742	0.313	349	0.242	6539	X-RAY DIFFRACTION	100
2.742-2.846	0.289	329	0.229	6350	X-RAY DIFFRACTION	99.9102
2.846-2.962	0.268	308	0.218	6073	X-RAY DIFFRACTION	99.9217
2.962-3.093	0.281	314	0.208	5900	X-RAY DIFFRACTION	99.9517
3.093-3.244	0.217	287	0.179	5581	X-RAY DIFFRACTION	99.8809
3.244-3.42	0.208	281	0.181	5344	X-RAY DIFFRACTION	99.9289
3.42-3.627	0.195	270	0.18	5017	X-RAY DIFFRACTION	99.8678
3.627-3.877	0.184	260	0.172	4731	X-RAY DIFFRACTION	99.581
3.877-4.187	0.191	213	0.155	4426	X-RAY DIFFRACTION	99.7849
4.187-4.587	0.141	195	0.135	4093	X-RAY DIFFRACTION	99.7441
4.587-5.127	0.178	202	0.137	3666	X-RAY DIFFRACTION	99.6907
5.127-5.918	0.179	173	0.147	3232	X-RAY DIFFRACTION	99.7364
5.918-7.244	0.181	136	0.159	2798	X-RAY DIFFRACTION	99.762

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