PDB-8j5l: Structure of GH1 Br2 beta-glucosidase E163Q mutant from bovine ru...

ID or keywords:

Entry

Database: PDB / ID: 8j5l

Title

Structure of GH1 Br2 beta-glucosidase E163Q mutant from bovine rumen metagenome

Components

Beta-glucosidase

Keywords

HYDROLASE / Glycoside hydrolase / GH1 / metagenome / beta-glucosidase

Function / homology

Function and homology information

beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.095 Å

Authors

Kaenying, W. / Kongsaeree, P.T. / Tagami, T.

Funding support

Thailand, 1items

Citation

Journal: Heliyon / Year: 2023
Title: Structural and mutational analysis of glycoside hydrolase family 1 Br2 beta-glucosidase derived from bovine rumen metagenome.
Authors: Kaenying, W. / Tagami, T. / Suwan, E. / Pitsanuwong, C. / Chomngam, S. / Okuyama, M. / Kongsaeree, P. / Kimura, A. / Kongsaeree, P.T.

History

Deposition	Apr 23, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 22, 2023	Provider: repository / Type: Initial release
Revision 1.1	Dec 13, 2023	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Jan 3, 2024	Group: Database references / Category: citation Item: _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Mar 12, 2025	Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details Item: _pdbx_database_related.content_type / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8j5l.cif.gz	383.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8j5l.ent.gz	301.3 KB	Display	PDB format
PDBx/mmJSON format	8j5l.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8j5l_validation.pdf.gz	496.6 KB	Display	wwPDB validaton report
Full document	8j5l_full_validation.pdf.gz	517 KB	Display
Data in XML	8j5l_validation.xml.gz	74.4 KB	Display
Data in CIF	8j5l_validation.cif.gz	95.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j5/8j5l ftp://data.pdbj.org/pub/pdb/validation_reports/j5/8j5l	HTTPS FTP

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Related structure data

Related structure data	8j3mC 8j5mC 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-glucosidase

B: Beta-glucosidase

C: Beta-glucosidase

D: Beta-glucosidase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	105.489, 113.416, 180.493
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LEU	LEU	A	A	-6 - 445	14 - 465
2	1	1	LEU	LEU	B	B	-6 - 445	14 - 465
3	2	2	PHE	PHE	A	A	3 - 444	23 - 464
4	2	2	PHE	PHE	C	C	3 - 444	23 - 464
5	3	3	PHE	PHE	A	A	3 - 444	23 - 464
6	3	3	PHE	PHE	D	D	3 - 444	23 - 464
7	4	4	PHE	PHE	B	B	3 - 444	23 - 464
8	4	4	PHE	PHE	C	C	3 - 444	23 - 464
9	5	5	PHE	PHE	B	B	3 - 444	23 - 464
10	5	5	PHE	PHE	D	D	3 - 444	23 - 464
11	6	6	PHE	PHE	C	C	3 - 445	23 - 465
12	6	6	PHE	PHE	D	D	3 - 445	23 - 465

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-glucosidase Mass: 53087.758 Da / Num. of mol.: 4 / Mutation: E163Q Source method: isolated from a genetically manipulated source Details: bovine rumen metagenome Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: BG / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1S5SJM8
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.58 Å³/Da / Density % sol: 51.62 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1M sodium acetate trihydrate pH 7.4, 1.6M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.095→50 Å / Num. obs: 115105 / % possible obs: 90.3 % / Redundancy: 4.9 % / B_iso Wilson estimate: 46.445 Å² / CC_1/2: 0.997 / R_rim(I) all: 0.109 / R_sym value: 0.097 / Net I/σ(I): 10.25
Reflection shell	Resolution: 2.095→2.22 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.55 / Num. unique obs: 19661 / CC_1/2: 0.625 / R_rim(I) all: 1.008 / R_sym value: 0.898 / % possible all: 96.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.095→48.139 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.93 / SU B: 7.697 / SU ML: 0.189 / Cross valid method: FREE R-VALUE / ESU R: 0.26 / ESU R Free: 0.207
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2613	1990	1.729 %
R_work	0.2267	113114	-
all	0.227	-	-
obs	-	115104	90.313 %

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: 48 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.681 Å²	0 Å²	0 Å²
2-	-	0.454 Å²	0 Å²
3-	-	-	0.227 Å²

Refinement step

Cycle: LAST / Resolution: 2.095→48.139 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14439	0	99	338	14876

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	14947
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	13496
X-RAY DIFFRACTION	r_angle_refined_deg	1.249	1.635	20286
X-RAY DIFFRACTION	r_angle_other_deg	1.205	1.58	31066
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.913	5	1786
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.016	23.032	818
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.9	15	2376
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.754	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	1834
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	17098
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3674
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	3114
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.174	0.2	13252
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	7354
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	6665
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.145	0.2	628
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.166	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.22	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.259	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.158	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	2.732	4.74	7156
X-RAY DIFFRACTION	r_mcbond_other	2.73	4.74	7155
X-RAY DIFFRACTION	r_mcangle_it	4.02	7.106	8938
X-RAY DIFFRACTION	r_mcangle_other	4.02	7.106	8939
X-RAY DIFFRACTION	r_scbond_it	2.721	4.955	7791
X-RAY DIFFRACTION	r_scbond_other	2.697	4.934	7744
X-RAY DIFFRACTION	r_scangle_it	4.217	7.338	11348
X-RAY DIFFRACTION	r_scangle_other	4.18	7.306	11277
X-RAY DIFFRACTION	r_lrange_it	5.94	54.222	17329
X-RAY DIFFRACTION	r_lrange_other	5.929	54.227	17298
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.046	0.05	15960
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.041	0.05	15730
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.041	0.05	15718
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.044	0.05	15677
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.04	0.05	15675
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.044	0.05	15805

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	0.046	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.046	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.04123	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.04123	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.0408	0.0501
3	6	D	X-RAY DIFFRACTION	Local ncs	0.0408	0.0501
4	7	B	X-RAY DIFFRACTION	Local ncs	0.04383	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.04383	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.04044	0.05009
5	10	D	X-RAY DIFFRACTION	Local ncs	0.04044	0.05009
6	11	C	X-RAY DIFFRACTION	Local ncs	0.04355	0.0501
6	12	D	X-RAY DIFFRACTION	Local ncs	0.04355	0.0501

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
2.095-2.15	0.339	150	0.328	8625	0.328	9321	0.705	0.719	94.1423	0.318
2.15-2.209	0.343	151	0.319	8785	0.32	9069	0.766	0.758	98.5335	0.305
2.209-2.273	0.416	40	0.359	2179	0.36	8862	0.631	0.691	25.0395	0.345
2.273-2.342	0.333	137	0.305	7645	0.306	8579	0.781	0.826	90.7099	0.275
2.342-2.419	0.327	143	0.284	8022	0.285	8318	0.825	0.837	98.1606	0.254
2.419-2.504	0.379	140	0.288	7745	0.29	8077	0.791	0.838	97.6229	0.254
2.504-2.598	0.329	129	0.271	7450	0.272	7772	0.851	0.873	97.5167	0.236
2.598-2.704	0.31	128	0.268	7156	0.269	7512	0.852	0.875	96.9649	0.232
2.704-2.823	0.299	132	0.271	6858	0.272	7205	0.867	0.867	97.016	0.24
2.823-2.961	0.318	112	0.27	6523	0.27	6897	0.849	0.863	96.2012	0.243
2.961-3.12	0.326	96	0.264	6192	0.265	6575	0.843	0.877	95.635	0.243
3.12-3.309	0.308	102	0.25	5803	0.251	6226	0.888	0.909	94.8442	0.237
3.309-3.536	0.269	98	0.236	5436	0.237	5881	0.904	0.924	94.0996	0.23
3.536-3.817	0.216	89	0.213	5034	0.213	5465	0.935	0.937	93.742	0.211
3.817-4.179	0.232	86	0.178	4645	0.179	5081	0.941	0.954	93.1116	0.185
4.179-4.668	0.181	70	0.164	4179	0.164	4589	0.953	0.962	92.591	0.177
4.668-5.382	0.197	63	0.166	3702	0.166	4077	0.962	0.965	92.3473	0.181
5.382-6.571	0.192	56	0.172	3178	0.173	3508	0.955	0.962	92.1893	0.187
6.571-9.207	0.185	44	0.161	2493	0.161	2755	0.959	0.966	92.0871	0.185
9.207-48.139	0.181	24	0.192	1464	0.192	1666	0.974	0.96	89.3157	0.253

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