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

ID or keywords:

Entry

Database: PDB / ID: 8yvs

Title

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

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 / glycosyltransferase activity / 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: 1.6 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	8yvs.cif.gz	1.8 MB	Display	PDBx/mmCIF format
PDB format	pdb8yvs.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	8yvs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8yvs_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	8yvs_full_validation.pdf.gz	2.8 MB	Display
Data in XML	8yvs_validation.xml.gz	92.8 KB	Display
Data in CIF	8yvs_validation.cif.gz	126.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yv/8yvs ftp://data.pdbj.org/pub/pdb/validation_reports/yv/8yvs	HTTPS FTP

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Related structure data

Related structure data	8yvrC 7fe3 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	#198 - Jun 2016 Beta-galactosidase similarity (1) #74 - Feb 2006 alpha-Amylase similarity (2) #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

231 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
462 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.991, 194.508, 112.19
Angle α, β, γ (deg.)	90, 117.214, 90
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-1224- 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: Chemical	ChemComp-CTS / CASTANOSPERMINE / (1S,6S,7R,8R,8AR)-1,6,7,8-TETRAHYDROXYINDOLIZIDINE Mass: 189.209 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₈H₁₅NO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1204 / 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: 2.6 Å³/Da / Density % sol: 52.7 %
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: 1.6→48.674 Å / Num. obs: 306692 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.062 / Net I/σ(I): 15.7
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 6.4 % / R_merge(I) obs: 0.867 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 15161 / CC_1/2: 0.802 / % possible all: 100

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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: 1.6→48.674 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.945 / WR_factor R_free: 0.212 / WR_factor R_work: 0.192 / SU B: 5.839 / SU ML: 0.085 / Average fsc free: 0.955 / Average fsc work: 0.9619 / Cross valid method: FREE R-VALUE / ESU R: 0.091 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2234	15471	5.045 %
R_work	0.2016	291189	-
all	0.203	-	-
obs	-	306660	99.89 %

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: 32.163 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.057 Å²	0 Å²	1.137 Å²
2-	-	-3.854 Å²	-0 Å²
3-	-	-	2.447 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→48.674 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15741	0	110	1204	17055

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	16266
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	15145
X-RAY DIFFRACTION	r_angle_refined_deg	1.654	1.815	22084
X-RAY DIFFRACTION	r_angle_other_deg	0.587	1.761	34962
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.741	5	1984
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.558	5	61
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.401	10	2756
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.605	10	759
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	2414
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	19060
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3728
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	3146
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	13933
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	7812
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	8237
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	1081
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.017	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.159	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.157	0.2	156
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.129	0.2	96
X-RAY DIFFRACTION	r_mcbond_it	1.308	1.458	7915
X-RAY DIFFRACTION	r_mcbond_other	1.308	1.458	7915
X-RAY DIFFRACTION	r_mcangle_it	1.894	2.617	9891
X-RAY DIFFRACTION	r_mcangle_other	1.894	2.617	9892
X-RAY DIFFRACTION	r_scbond_it	1.966	1.658	8351
X-RAY DIFFRACTION	r_scbond_other	1.966	1.658	8352
X-RAY DIFFRACTION	r_scangle_it	2.998	2.95	12188
X-RAY DIFFRACTION	r_scangle_other	2.998	2.95	12189
X-RAY DIFFRACTION	r_lrange_it	3.822	14.274	18527
X-RAY DIFFRACTION	r_lrange_other	3.792	14.23	18428
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.071	0.05	22664
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.06	0.05	22805
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.067	0.05	22795

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	0.0714	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.0714	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06034	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06034	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.0665	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.0665	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
1.6-1.642	0.309	1101	0.293	21563	0.294	22667	0.919	0.909	99.9868	0.275
1.642-1.686	0.266	1111	0.271	20951	0.27	22062	0.928	0.931	100	0.252
1.686-1.735	0.265	1052	0.255	20343	0.256	21474	0.93	0.942	99.6321	0.232
1.735-1.789	0.256	1108	0.241	19731	0.242	20843	0.942	0.952	99.9808	0.218
1.789-1.847	0.251	1051	0.229	19127	0.23	20184	0.946	0.958	99.9703	0.203
1.847-1.912	0.244	980	0.214	18637	0.215	19624	0.954	0.966	99.9643	0.188
1.912-1.984	0.229	916	0.196	18013	0.198	18936	0.961	0.972	99.963	0.172
1.984-2.065	0.224	889	0.196	17173	0.197	18066	0.963	0.973	99.9779	0.174
2.065-2.156	0.223	863	0.198	16616	0.199	17498	0.964	0.973	99.8914	0.176
2.156-2.262	0.211	848	0.19	15765	0.191	16618	0.968	0.976	99.9699	0.171
2.262-2.384	0.215	853	0.188	14954	0.19	15822	0.967	0.976	99.9052	0.17
2.384-2.528	0.224	721	0.19	14285	0.192	15019	0.966	0.976	99.9134	0.173
2.528-2.702	0.216	676	0.186	13429	0.188	14116	0.969	0.978	99.9221	0.172
2.702-2.918	0.217	668	0.184	12482	0.186	13166	0.97	0.978	99.8785	0.175
2.918-3.195	0.202	654	0.192	11403	0.192	12099	0.974	0.976	99.6529	0.187
3.195-3.57	0.216	586	0.198	10289	0.199	10933	0.972	0.977	99.4695	0.198
3.57-4.119	0.205	462	0.185	9230	0.186	9701	0.975	0.98	99.9072	0.194
4.119-5.035	0.191	421	0.168	7752	0.169	8177	0.979	0.984	99.9511	0.184
5.035-7.083	0.249	313	0.223	6030	0.225	6358	0.974	0.98	99.7641	0.241
7.083-48.674	0.253	198	0.253	3417	0.253	3621	0.974	0.974	99.8343	0.27

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	0.4022	0.0488	-0.0107	1.0039	0.4155	0.4259	-0.0115	-0.0315	0.0047	-0.0053	-0.0507	0.218	-0.0228	-0.1033	0.0621	0.1134	0.0095	0.0335	0.169	0.0187	0.0626	-32.9259	-0.2762	12.3709
2	0.2443	-0.0267	0.0467	1.4487	-0.6446	0.8454	-0.0009	-0.129	0.0331	0.3353	-0.1296	-0.248	-0.1015	0.1254	0.1306	0.1723	-0.0208	-0.022	0.241	0.0061	0.0724	11.0298	0.6713	32.9865
3	1.1219	0.1082	0.021	0.428	-0.0867	0.2308	0.0312	-0.1085	-0.1251	0.1058	-0.0149	-0.0112	0.0582	-0.0187	-0.0163	0.1877	-0.0159	0.013	0.1524	0.009	0.0183	-10.2364	-42.3996	22.8297

Refinement TLS group

Selection: ALL

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