PDB-7bwb: Bombyx mori GH32 beta-fructofuranosidase BmSUC1

ID or keywords:

Entry

Database: PDB / ID: 7bwb

Title

Bombyx mori GH32 beta-fructofuranosidase BmSUC1

Components

Beta-fructofuranosidase

Keywords

HYDROLASE / GLYCOSIDE HYDROLASE / SUCROSE / BETA-PROPELLER / HORIZONTAL GENE TRANSFER

Function / homology

Function and homology information

beta-fructofuranosidase activity / beta-fructofuranosidase / carbohydrate metabolic process / cytoplasm
Similarity search - Function

Biological species

Bombyx mori (domestic silkworm)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Miyazaki, T. / Oba, N.

Funding support

Japan, 1items

Citation

Journal: Insect Biochem.Mol.Biol. / Year: 2020
Title: Structural insight into the substrate specificity of Bombyx mori beta-fructofuranosidase belonging to the glycoside hydrolase family 32.
Authors: Miyazaki, T. / Oba, N. / Park, E.Y.

History

Deposition	Apr 14, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 4, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 18, 2020	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Nov 29, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7bwb.cif.gz	199.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7bwb.ent.gz	154.1 KB	Display	PDB format
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Validation report

Summary document	7bwb_validation.pdf.gz	428.4 KB	Display	wwPDB validaton report
Full document	7bwb_full_validation.pdf.gz	431.7 KB	Display
Data in XML	7bwb_validation.xml.gz	19.4 KB	Display
Data in CIF	7bwb_validation.cif.gz	28.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bw/7bwb ftp://data.pdbj.org/pub/pdb/validation_reports/bw/7bwb	HTTPS FTP

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Related structure data

Related structure data	7bwcC 1uypS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7bwc-d 3h72-1 4udq-2 2nt0-3 2wy1-2 3h73-1 6i3i-d 7kho-1 2bvh-3 2yg7-2 Search similar-shape structures by Omokage search (details) 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-fructofuranosidase

56.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	94.752, 119.308, 100.275
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-669- HOH

#1: Protein	Beta-fructofuranosidase Mass: 56067.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The sequence is registered GenBank with an accession code of BCD5765 Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: BmSuc1, Suc1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A6F8Z6Y2*PLUS, beta-fructofuranosidase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Beta-fructofuranosidase

Mass: 56067.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence is registered GenBank with an accession code of BCD5765
Source: (gene. exp.)

Bombyx mori (domestic silkworm) / Gene: BmSuc1, Suc1 / Plasmid: pET28a / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A6F8Z6Y2*PLUS, beta-fructofuranosidase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.33 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 13% PEG 3350, 40 mM citric acid, 60 mM Bis-Tris propane

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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: Mar 6, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 52834 / % possible obs: 99.9 % / Redundancy: 6 % / R_merge(I) obs: 0.051 / Net I/σ(I): 17
Reflection shell	Resolution: 1.8→1.9 Å / R_merge(I) obs: 0.607 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7635

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
SCALA		data scaling
MrBUMP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1UYP

1uyp

Resolution: 1.8→42.872 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.959 / SU B: 8.311 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.11
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2131	2559	4.863 %
R_work	0.1678	-	-
all	0.17	-	-
obs	-	52623	99.518 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 39.454 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.91 Å²	-0 Å²	0 Å²
2-	-	-1.012 Å²	-0 Å²
3-	-	-	-3.899 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→42.872 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3777	0	0	188	3965

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	3902
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	3401
X-RAY DIFFRACTION	r_angle_refined_deg	1.523	1.643	5314
X-RAY DIFFRACTION	r_angle_other_deg	1.292	1.573	7914
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.546	5	467
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.94	23.045	220
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.227	15	617
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.985	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	474
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4423
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	878
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	623
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	3168
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	1802
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1698
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.119	0.2	183
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.081	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.227	0.2	21
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.274	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	1.71	1.864	1859
X-RAY DIFFRACTION	r_mcbond_other	1.71	1.863	1858
X-RAY DIFFRACTION	r_mcangle_it	2.192	2.796	2323
X-RAY DIFFRACTION	r_mcangle_other	2.192	2.797	2324
X-RAY DIFFRACTION	r_scbond_it	1.922	2.089	2043
X-RAY DIFFRACTION	r_scbond_other	1.922	2.09	2043
X-RAY DIFFRACTION	r_scangle_it	2.411	3.054	2989
X-RAY DIFFRACTION	r_scangle_other	2.411	3.054	2989
X-RAY DIFFRACTION	r_lrange_it	2.876	21.629	4256
X-RAY DIFFRACTION	r_lrange_other	2.869	21.452	4229
X-RAY DIFFRACTION	r_rigid_bond_restr	2.096	3	7303

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 (%)
1.8-1.847	0.33	187	0.276	3672	X-RAY DIFFRACTION	99.7673
1.847-1.897	0.287	176	0.245	3590	X-RAY DIFFRACTION	99.7088
1.897-1.952	0.308	172	0.228	3485	X-RAY DIFFRACTION	99.7001
1.952-2.012	0.254	172	0.2	3379	X-RAY DIFFRACTION	99.8875
2.012-2.078	0.264	162	0.195	3278	X-RAY DIFFRACTION	99.768
2.078-2.151	0.231	167	0.185	3173	X-RAY DIFFRACTION	99.9402
2.151-2.232	0.196	186	0.155	3067	X-RAY DIFFRACTION	99.9079
2.232-2.323	0.199	178	0.155	2906	X-RAY DIFFRACTION	99.6124
2.323-2.427	0.223	157	0.165	2836	X-RAY DIFFRACTION	99.667
2.427-2.545	0.279	129	0.181	2723	X-RAY DIFFRACTION	99.4768
2.545-2.682	0.243	129	0.17	2576	X-RAY DIFFRACTION	99.339
2.682-2.845	0.234	97	0.171	2475	X-RAY DIFFRACTION	98.885
2.845-3.041	0.234	114	0.176	2284	X-RAY DIFFRACTION	98.9682
3.041-3.284	0.186	122	0.176	2132	X-RAY DIFFRACTION	99.1205
3.284-3.597	0.22	112	0.171	1975	X-RAY DIFFRACTION	99.0978
3.597-4.02	0.173	80	0.151	1812	X-RAY DIFFRACTION	99.0576
4.02-4.64	0.157	77	0.128	1598	X-RAY DIFFRACTION	99.3476
4.64-5.677	0.171	60	0.132	1371	X-RAY DIFFRACTION	98.7578
5.677-8.005	0.209	47	0.164	1094	X-RAY DIFFRACTION	99.5637
8.005-42.872	0.199	35	0.168	638	X-RAY DIFFRACTION	98.9706

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	21.7051	5.3687	-12.3447	16.334	-9.8087	24.9149	-0.1924	1.3744	0.0993	0.6982	-0.2791	-0.3656	0.6502	0.2397	0.4715	0.3802	-0.1391	0.0213	0.2672	-0.0947	0.3323	30.636	47.131	17.09
2	2.1798	-0.8887	-1.626	1.8663	0.6191	3.312	0.4733	-0.3865	0.6734	-0.0532	0.2042	-0.4173	-1.101	0.6248	-0.6775	0.4174	-0.2507	0.2274	0.1943	-0.2021	0.4547	26.519	31.369	15.161
3	1.1213	-0.3227	-0.9858	0.8492	0.3258	1.9449	0.0543	-0.1228	0.1784	-0.0784	0.1268	-0.1199	-0.1689	0.2988	-0.181	0.0254	-0.0498	0.0164	0.1115	-0.0418	0.21	21.825	14.442	11.212

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	25 - 32
2	X-RAY DIFFRACTION	2	ALL	A	33 - 143
3	X-RAY DIFFRACTION	3	ALL	A	144 - 488

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