PDB-8yvr: Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacteri...

ID or keywords:

Entry

Database: PDB / ID: 8yvr

Title

Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with 1-deoxynojirimycin

Components

Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65

Keywords

HYDROLASE / glycoside hydrolase / GH65 / kojibiose / (alpha/alpha)6-barrel / inhibitor / glucosidase / dextran

Function / homology

Function and homology information

kojibiose hydrolase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / periplasmic space
Similarity search - Function

Biological species

Flavobacterium johnsoniae UW101 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Nakamura, S. / Miyazaki, T.

Funding support

Japan, 2items

Citation

Journal: Biosci.Biotechnol.Biochem. / Year: 2024
Title: Structural insights into the inhibition mechanism of glucosidase inhibitors toward kojibiose hydrolase belonging to glycoside hydrolase family 65.
Authors: Nakamura, S. / Miyazaki, T.

History

Deposition	Mar 29, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8yvr.cif.gz	1.8 MB	Display	PDBx/mmCIF format
PDB format	pdb8yvr.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	8yvr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yv/8yvr ftp://data.pdbj.org/pub/pdb/validation_reports/yv/8yvr	HTTPS FTP

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Related structure data

Related structure data	8yvsC 7fe3 7fe4 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
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (3) #198 - Jun 2016 Beta-galactosidase similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65

B: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65

C: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65

hetero molecules

230 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65

B: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65

C: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65

hetero molecules

A: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65

B: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65

C: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65

hetero molecules

defined by author&software
Evidence: gel filtration
460 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.841, 194.371, 112.129
Angle α, β, γ (deg.)	90, 116.541, 90
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-1131- HOH

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

NCS domain segments:

Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: HIS / End label comp-ID: HIS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 23 - 681 / Label seq-ID: 20 - 678

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3

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

#1: Protein	Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65 / alpha-1 / 2-glucosidase Mass: 76489.219 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacterium johnsoniae UW101 (bacteria) Gene: Fjoh_4428 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A5FBJ5
#2: Sugar	ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE Type: D-saccharide / Mass: 163.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄ / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 886 / 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: 2.61 Å³/Da / Density % sol: 52.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 300 mM ammonium citrate, pH 7.0-8.0, 10 mM TCEP, 12% PEG 3350 PH range: 7.0-8.0

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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 S 6M / Detector: PIXEL / Date: Oct 25, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→48.64 Å / Num. obs: 184040 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC_1/2: 0.997 / R_merge(I) obs: 0.099 / Net I/σ(I): 10.5
Reflection shell	Resolution: 1.9→1.93 Å / R_merge(I) obs: 0.498 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 9083 / CC_1/2: 0.944

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→48.64 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.917 / SU B: 12.299 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / ESU R: 0.194 / ESU R Free: 0.165
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2762	9198	5.017 %
R_work	0.2539	174153	-
all	0.255	-	-
obs	-	183351	99.543 %

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: 39.476 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.778 Å²	0 Å²	0.554 Å²
2-	-	-2.402 Å²	-0 Å²
3-	-	-	1.752 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→48.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15741	0	41	886	16668

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	16167
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	15044
X-RAY DIFFRACTION	r_angle_refined_deg	1.483	1.814	21943
X-RAY DIFFRACTION	r_angle_other_deg	0.516	1.762	34709
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.979	5	1974
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.37	5	60
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.129	10	2748
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.556	10	756
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	2385
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	19002
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3714
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	3303
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	13916
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	7722
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	8115
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	921
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.041	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.183	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.149	0.2	133
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.186	0.2	44
X-RAY DIFFRACTION	r_mcbond_it	0.969	1.325	7905
X-RAY DIFFRACTION	r_mcbond_other	0.969	1.325	7905
X-RAY DIFFRACTION	r_mcangle_it	1.549	2.378	9876
X-RAY DIFFRACTION	r_mcangle_other	1.549	2.378	9877
X-RAY DIFFRACTION	r_scbond_it	1.208	1.438	8262
X-RAY DIFFRACTION	r_scbond_other	1.208	1.438	8263
X-RAY DIFFRACTION	r_scangle_it	1.947	2.59	12067
X-RAY DIFFRACTION	r_scangle_other	1.947	2.59	12068
X-RAY DIFFRACTION	r_lrange_it	5.139	12.897	18428
X-RAY DIFFRACTION	r_lrange_other	5.117	12.551	18285
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.062	0.05	22681
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.06	0.05	22731
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.051	0.05	22874

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	0.06165	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06165	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05969	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.05969	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05086	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.05086	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
1.9-1.949	0.372	685	0.334	12914	0.335	13603	0.893	0.908	99.9706	0.301
1.949-2.003	0.326	683	0.311	12576	0.312	13265	0.916	0.92	99.9548	0.278
2.003-2.061	0.351	615	0.307	12232	0.309	12852	0.91	0.926	99.9611	0.274
2.061-2.124	0.313	628	0.291	11841	0.292	12480	0.924	0.936	99.9119	0.26
2.124-2.193	0.301	595	0.278	11526	0.279	12128	0.937	0.944	99.9423	0.25
2.193-2.27	0.283	581	0.259	11130	0.261	11720	0.944	0.952	99.9232	0.233
2.27-2.356	0.306	613	0.257	10692	0.26	11321	0.939	0.955	99.8587	0.233
2.356-2.452	0.294	587	0.253	10296	0.255	10908	0.944	0.959	99.7708	0.23
2.452-2.56	0.282	513	0.247	9904	0.248	10453	0.948	0.962	99.6556	0.224
2.56-2.685	0.291	506	0.256	9428	0.258	9979	0.947	0.962	99.5491	0.234
2.685-2.83	0.3	473	0.252	8951	0.254	9490	0.947	0.962	99.3045	0.234
2.83-3.001	0.282	418	0.253	8532	0.254	9000	0.951	0.962	99.4444	0.239
3.001-3.207	0.262	408	0.254	7992	0.255	8487	0.955	0.965	98.9749	0.244
3.207-3.463	0.267	406	0.261	7388	0.261	7876	0.958	0.966	98.9589	0.255
3.463-3.791	0.263	357	0.247	6833	0.248	7271	0.962	0.97	98.886	0.245
3.791-4.236	0.253	325	0.226	6132	0.227	6583	0.962	0.972	98.086	0.233
4.236-4.885	0.204	283	0.203	5430	0.203	5804	0.977	0.977	98.4321	0.223
4.885-5.967	0.236	250	0.235	4620	0.235	4928	0.971	0.976	98.8231	0.257
5.967-8.377	0.254	140	0.248	3673	0.249	3831	0.976	0.975	99.5302	0.268
8.377-48.64	0.216	132	0.193	2063	0.195	2199	0.976	0.978	99.8181	0.208

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.5459	0.0044	-0.1156	1.1432	0.379	0.4447	0.0159	-0.0427	-0.0296	0.0307	-0.0492	0.1414	-0.0192	-0.139	0.0333	0.0111	0.0116	0.0701	0.0651	0.0262	0.5851	-33.0558	-0.2483	12.4443
2	0.3146	0.0684	0.0429	1.0312	-0.3647	0.7676	0.0343	-0.1976	0.0618	0.4075	-0.1294	-0.103	-0.0621	0.1824	0.0951	0.1797	-0.0297	0.0335	0.1831	0.0082	0.5757	11.5367	0.5529	33.1231
3	0.9659	-0.0063	0.0576	0.3962	-0.0872	0.2684	0.0126	-0.176	-0.0666	0.1372	-0.0061	-0.0177	0.0816	-0.022	-0.0065	0.121	-0.018	0.061	0.0357	0.0039	0.52	-10.1413	-42.4781	22.9418

Refinement TLS group

Selection: ALL

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