PDB-8kap: Glycoside hydrolase family 1 beta-glucosidase from Streptomyces g...

ID or keywords:

Entry

Database: PDB / ID: 8kap

Title

Glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus (ligand-free)

Components

SGR_2426

Keywords

HYDROLASE / beta-Glucosidase

Function / homology

DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL

Function and homology information

Biological species

Streptomyces griseus subsp. griseus NBRC 13350 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Kumakura, H. / Motouchi, S. / Nakai, H. / Nakajima, M.

Funding support

Japan, 1items

Citation

Journal: To Be Published
Title: Identification of beta-1,2-glucan-associated glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus
Authors: Kumakura, H. / Motouchi, S. / Nakai, H. / Nakajima, M.

History

Deposition	Aug 3, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 7, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8kap.cif.gz	317.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8kap.ent.gz	249.5 KB	Display	PDB format
PDBx/mmJSON format	8kap.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8kap_validation.pdf.gz	497.6 KB	Display	wwPDB validaton report
Full document	8kap_full_validation.pdf.gz	508.5 KB	Display
Data in XML	8kap_validation.xml.gz	55.9 KB	Display
Data in CIF	8kap_validation.cif.gz	76.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ka/8kap ftp://data.pdbj.org/pub/pdb/validation_reports/ka/8kap	HTTPS FTP

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Related structure data

Related structure data	8kaqC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: SGR_2426

B: SGR_2426

C: SGR_2426

D: SGR_2426

hetero molecules

185 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)	96.858, 97.756, 184.874
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	SGR_2426 Mass: 45762.668 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseus subsp. griseus NBRC 13350 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / References: beta-glucosidase

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Non-polymers , 5 types, 311 molecules

#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.5 Å³/Da / Density % sol: 50.88 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris (pH 5.5), 0.2 M ammonium acetate, 15% (w/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 7, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→48.43 Å / Num. obs: 89749 / % possible obs: 100 % / Redundancy: 6.6 % / CC_1/2: 0.991 / Net I/σ(I): 8.8
Reflection shell	Resolution: 2.2→2.24 Å / Num. unique obs: 4548 / CC_1/2: 0.685 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
XDS		data reduction
MOLREP		phasing
ARP/wARP		model building
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→46.261 Å / Cor.coef. F_o:F_c: 0.914 / Cor.coef. F_o:F_c free: 0.898 / Cross valid method: FREE R-VALUE / ESU R: 0.314 / ESU R Free: 0.221
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2568	4438	4.949 %
R_work	0.232	85230	-
all	0.233	-	-
obs	-	89668	99.936 %

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: 25.474 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.448 Å²	0 Å²	-0 Å²
2-	-	-2.656 Å²	0 Å²
3-	-	-	3.105 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→46.261 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12240	0	113	302	12655

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	12700
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	11414
X-RAY DIFFRACTION	r_angle_refined_deg	0.863	1.664	17356
X-RAY DIFFRACTION	r_angle_other_deg	0.54	1.582	26203
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.464	5	1570
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.976	5	108
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.719	10	1773
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.108	10	612
X-RAY DIFFRACTION	r_chiral_restr	0.047	0.2	1857
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	15558
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	3050
X-RAY DIFFRACTION	r_nbd_refined	0.185	0.2	2771
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.209	0.2	10968
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	6257
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	6284
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.109	0.2	514
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.033	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.102	0.2	36
X-RAY DIFFRACTION	r_nbd_other	0.175	0.2	86
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.104	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	0.41	2.65	6292
X-RAY DIFFRACTION	r_mcbond_other	0.41	2.65	6292
X-RAY DIFFRACTION	r_mcangle_it	0.772	4.765	7858
X-RAY DIFFRACTION	r_mcangle_other	0.772	4.766	7859
X-RAY DIFFRACTION	r_scbond_it	0.24	2.64	6408
X-RAY DIFFRACTION	r_scbond_other	0.24	2.64	6409
X-RAY DIFFRACTION	r_scangle_it	0.483	4.846	9498
X-RAY DIFFRACTION	r_scangle_other	0.483	4.846	9499
X-RAY DIFFRACTION	r_lrange_it	1.562	25.324	14420
X-RAY DIFFRACTION	r_lrange_other	1.562	25.324	14421

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
2.2-2.257	0.361	316	0.313	6231	0.315	6548	0.885	0.918	99.9847	0.287
2.257-2.319	0.339	322	0.3	6063	0.302	6386	0.905	0.927	99.9843	0.271
2.319-2.386	0.325	321	0.298	5865	0.299	6189	0.918	0.932	99.9515	0.268
2.386-2.459	0.321	250	0.288	5809	0.289	6062	0.905	0.938	99.9505	0.259
2.459-2.539	0.3	259	0.282	5572	0.283	5832	0.936	0.941	99.9828	0.252
2.539-2.628	0.296	261	0.262	5410	0.264	5674	0.934	0.95	99.9471	0.23
2.628-2.727	0.318	265	0.252	5183	0.255	5449	0.929	0.955	99.9817	0.224
2.727-2.838	0.286	258	0.245	5042	0.247	5300	0.945	0.958	100	0.219
2.838-2.964	0.302	288	0.245	4789	0.248	5080	0.936	0.958	99.9409	0.216
2.964-3.108	0.255	240	0.243	4604	0.243	4850	0.955	0.96	99.8763	0.22
3.108-3.275	0.276	238	0.244	4390	0.245	4628	0.953	0.96	100	0.221
3.275-3.473	0.244	222	0.236	4158	0.236	4383	0.964	0.965	99.9316	0.22
3.473-3.711	0.226	254	0.219	3878	0.219	4132	0.97	0.97	100	0.201
3.711-4.006	0.209	203	0.189	3652	0.19	3857	0.972	0.977	99.9481	0.172
4.006-4.385	0.179	184	0.181	3391	0.181	3578	0.982	0.98	99.9162	0.163
4.385-4.897	0.217	123	0.178	3125	0.179	3252	0.976	0.982	99.877	0.161
4.897-5.644	0.196	154	0.195	2728	0.195	2884	0.978	0.979	99.9306	0.176
5.644-6.887	0.22	139	0.189	2333	0.191	2472	0.976	0.979	100	0.169
6.887-9.634	0.164	84	0.162	1881	0.162	1967	0.981	0.983	99.8983	0.151
9.634-46.261	0.302	57	0.209	1126	0.213	1188	0.897	0.97	99.5791	0.206

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