PDB-8wg0: Crystal structure of GH97 glucodextranase from Flavobacterium joh...

ID or keywords:

Entry

Database: PDB / ID: 8wg0

Title

Crystal structure of GH97 glucodextranase from Flavobacterium johnsoniae in complex with glucose

Components

Candidate alpha-glucosidase Glycoside hydrolase family 97

Keywords

HYDROLASE / GLYCOSIDE HYDROLASE / GH97 / DEXTRAN / TIM-BARREL / ISOMALTOSE / NIGEROSE

Function / homology

Function and homology information

carbohydrate binding / hydrolase activity / metal ion binding
Similarity search - Function

Biological species

Flavobacterium johnsoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Kurata, R. / Nakamura, S. / Miyazaki, T.

Funding support

Japan, 2items

Citation

Journal: Febs J. / Year: 2024
Title: Structural insights into alpha-(1→6)-linkage preference of GH97 glucodextranase from Flavobacterium johnsoniae.
Authors: Nakamura, S. / Kurata, R. / Miyazaki, T.

History

Deposition	Sep 20, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 31, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8wg0.cif.gz	2.6 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	8wg0_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	8wg0_full_validation.pdf.gz	2.3 MB	Display
Data in XML	8wg0_validation.xml.gz	98.6 KB	Display
Data in CIF	8wg0_validation.cif.gz	141 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wg/8wg0 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/8wg0	HTTPS FTP

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Related structure data

Related structure data	8wg1C 8wg2C 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) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1)

Deposited unit

A: Candidate alpha-glucosidase Glycoside hydrolase family 97

B: Candidate alpha-glucosidase Glycoside hydrolase family 97

C: Candidate alpha-glucosidase Glycoside hydrolase family 97

D: Candidate alpha-glucosidase Glycoside hydrolase family 97

hetero molecules

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

1

A: Candidate alpha-glucosidase Glycoside hydrolase family 97

B: Candidate alpha-glucosidase Glycoside hydrolase family 97

hetero molecules

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

2

C: Candidate alpha-glucosidase Glycoside hydrolase family 97

D: Candidate alpha-glucosidase Glycoside hydrolase family 97

hetero molecules

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

Unit cell

Length a, b, c (Å)	307.927, 103.691, 95.671
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

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: SER / Beg label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	VAL	VAL	20 - 700	23 - 703
2	1	1	VAL	VAL	20 - 700	23 - 703
3	2	2	ALA	ALA	20 - 701	23 - 704
4	2	2	ALA	ALA	20 - 701	23 - 704
5	3	3	VAL	VAL	20 - 700	23 - 703
6	3	3	VAL	VAL	20 - 700	23 - 703
7	4	4	VAL	VAL	20 - 700	23 - 703
8	4	4	VAL	VAL	20 - 700	23 - 703
9	5	5	VAL	VAL	20 - 700	23 - 703
10	5	5	VAL	VAL	20 - 700	23 - 703
11	6	6	VAL	VAL	20 - 700	23 - 703
12	6	6	VAL	VAL	20 - 700	23 - 703

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

Candidate alpha-glucosidase Glycoside hydrolase family 97

Mass: 80531.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101) (bacteria)
Strain: ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101
Gene: Fjoh_4429 / Plasmid: pET28a / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5FBI0, glucan 1,6-alpha-glucosidase

#2: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

#3: Sugar

ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#4: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 848 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 12% PEG20000, 200 mM sodium cacodylate buffer (pH 6.0), 200 mM magnesium acetate, 10 mM glucose

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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: Dec 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.95→49.13 Å / Num. obs: 223030 / % possible obs: 100 % / Redundancy: 13.5 % / CC_1/2: 1 / R_merge(I) obs: 0.09 / R_pim(I) all: 0.037 / R_rim(I) all: 0.097 / Net I/σ(I): 23
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 13.6 % / R_merge(I) obs: 1.471 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10951 / CC_1/2: 0.836 / R_pim(I) all: 0.594 / R_rim(I) all: 1.588 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→49.13 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.945 / SU B: 10.284 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.163 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2289	10922	4.898 %
R_work	0.189	212056	-
all	0.191	-	-
obs	-	222978	99.975 %

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: 41.206 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.013 Å²	-0 Å²	0 Å²
2-	-	3.232 Å²	-0 Å²
3-	-	-	-0.219 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→49.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21871	0	80	848	22799

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	22550
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	20487
X-RAY DIFFRACTION	r_angle_refined_deg	1.902	1.652	30571
X-RAY DIFFRACTION	r_angle_other_deg	0.632	1.577	47214
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.51	5	2727
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.208	5	93
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.167	10	3709
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.894	10	1119
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	3223
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	26385
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5436
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	4050
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	19339
X-RAY DIFFRACTION	r_nbtor_refined	0.187	0.2	11088
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	12116
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	1118
X-RAY DIFFRACTION	r_metal_ion_refined	0.113	0.2	16
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.144	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	70
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.169	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	2.785	2.224	10905
X-RAY DIFFRACTION	r_mcbond_other	2.785	2.224	10905
X-RAY DIFFRACTION	r_mcangle_it	3.602	3.978	13624
X-RAY DIFFRACTION	r_mcangle_other	3.602	3.978	13625
X-RAY DIFFRACTION	r_scbond_it	3.486	2.428	11645
X-RAY DIFFRACTION	r_scbond_other	3.486	2.428	11646
X-RAY DIFFRACTION	r_scangle_it	4.783	4.336	16944
X-RAY DIFFRACTION	r_scangle_other	4.783	4.336	16945
X-RAY DIFFRACTION	r_lrange_it	5.923	21.546	25566
X-RAY DIFFRACTION	r_lrange_other	5.922	21.453	25421
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.073	0.05	23640
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.058	0.05	23930
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.07	0.05	23747
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.07	0.05	23713
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.069	0.05	23688
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.064	0.05	23815

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	0.07267	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07267	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05818	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.05818	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06969	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06969	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.07023	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.07023	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.06924	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.06924	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06419	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.06419	0.0501

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 (%)
1.95-2.001	0.33	809	0.311	15485	X-RAY DIFFRACTION	99.9755
2.001-2.055	0.304	788	0.288	15093	X-RAY DIFFRACTION	99.9811
2.055-2.115	0.293	728	0.271	14803	X-RAY DIFFRACTION	99.9871
2.115-2.18	0.277	726	0.252	14300	X-RAY DIFFRACTION	99.9667
2.18-2.251	0.269	709	0.23	13840	X-RAY DIFFRACTION	99.9656
2.251-2.33	0.276	678	0.217	13469	X-RAY DIFFRACTION	99.9929
2.33-2.418	0.26	681	0.204	12936	X-RAY DIFFRACTION	99.9853
2.418-2.516	0.252	636	0.204	12551	X-RAY DIFFRACTION	99.9924
2.516-2.628	0.251	565	0.195	12034	X-RAY DIFFRACTION	99.9841
2.628-2.756	0.253	619	0.193	11459	X-RAY DIFFRACTION	99.9917
2.756-2.904	0.248	571	0.191	10947	X-RAY DIFFRACTION	100
2.904-3.08	0.235	557	0.193	10340	X-RAY DIFFRACTION	99.9908
3.08-3.291	0.233	509	0.196	9763	X-RAY DIFFRACTION	99.9708
3.291-3.554	0.241	477	0.203	9103	X-RAY DIFFRACTION	99.9896
3.554-3.891	0.222	452	0.188	8374	X-RAY DIFFRACTION	100
3.891-4.347	0.179	412	0.143	7669	X-RAY DIFFRACTION	100
4.347-5.013	0.165	364	0.125	6756	X-RAY DIFFRACTION	100
5.013-6.123	0.178	258	0.141	5845	X-RAY DIFFRACTION	100
6.123-8.593	0.168	247	0.136	4559	X-RAY DIFFRACTION	100
8.593-49.13	0.208	136	0.165	2730	X-RAY DIFFRACTION	99.8954

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	1.8977	0.5532	0.4246	0.6278	0.0339	0.7701	-0.116	0.281	-0.0241	-0.0186	0.0811	-0.0471	-0.0833	0.1025	0.0349	0.0663	0.0094	0.0038	0.0949	0.0107	0.0083	65.0921	27.3983	-19.965
2	2.0572	0.1619	0.2533	0.4395	0.1301	1.0543	0.0798	0.0607	-0.5544	0.0712	0.0133	-0.1703	-0.061	0.0394	-0.0931	0.0987	-0.0136	-0.0994	0.0646	0.0331	0.318	110.5703	22.6806	2.6389
3	1.1102	-0.1204	-0.1644	0.5704	0.0452	0.8015	-0.0315	0.1342	-0.1177	-0.0022	-0.0308	0.0295	0.0557	0.0587	0.0623	0.0903	-0.011	0.0179	0.1344	-0.0497	0.0302	37.8461	20.7062	27.5462
4	1.3072	-0.361	0.1042	0.8103	-0.3989	1.1825	-0.0884	-0.0821	-0.3203	0.2933	0.1835	0.3123	-0.106	-0.1799	-0.0951	0.207	0.0319	0.1576	0.1029	0.0419	0.2043	-7.9796	26.3103	49.1714

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	20 - 804
2	X-RAY DIFFRACTION	2		B	20 - 802
3	X-RAY DIFFRACTION	3		C	20 - 804
4	X-RAY DIFFRACTION	4		D	20 - 803

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