PDB-7bwc: Bombyx mori GH32 beta-fructofuranosidase BmSUC1 mutant D63A in co...

ID or keywords:

Entry

Database: PDB / ID: 7bwc

Title

Bombyx mori GH32 beta-fructofuranosidase BmSUC1 mutant D63A in complex with sucrose

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: 1.95 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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Download

PDBx/mmCIF format	7bwc.cif.gz	194.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7bwc.ent.gz	149.2 KB	Display	PDB format
PDBx/mmJSON format	7bwc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7bwc_validation.pdf.gz	843.1 KB	Display	wwPDB validaton report
Full document	7bwc_full_validation.pdf.gz	846.5 KB	Display
Data in XML	7bwc_validation.xml.gz	19.4 KB	Display
Data in CIF	7bwc_validation.cif.gz	27.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bw/7bwc ftp://data.pdbj.org/pub/pdb/validation_reports/bw/7bwc	HTTPS FTP

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Related structure data

Related structure data	7bwbC 1uypS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7bwb-d 5l0v-d 4tsr-d 6ymn-1 1uyp-1 4udq-2 4p53-d 2vak-12 4udr-1 1nkq-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

hetero molecules

56.4 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)	96.522, 118.459, 101.285
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-638- HOH

#1: Protein

Beta-fructofuranosidase

Mass: 56023.266 Da / Num. of mol.: 1 / Mutation: D63A
Source method: isolated from a genetically manipulated source
Details: The sequence is registered GenBank with an accession code of BCD57653
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: Polysaccharide

beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.58 Å³/Da / Density % sol: 52.36 %
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: Nov 24, 2019
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→50 Å / Num. obs: 42574 / % possible obs: 99.9 % / Redundancy: 6.4 % / R_merge(I) obs: 0.063 / Net I/σ(I): 13.1
Reflection shell	Resolution: 1.95→2.06 Å / R_merge(I) obs: 0.661 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6137

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1UYP

1uyp

Resolution: 1.95→41.975 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.943 / SU B: 11.908 / SU ML: 0.154 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.158
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2469	2032	4.971 %
R_work	0.2159	-	-
all	0.217	-	-
obs	-	40878	95.98 %

Solvent computation

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

Displacement parameters

B_iso mean: 50.272 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.133 Å²	-0 Å²	-0 Å²
2-	-	-3.174 Å²	-0 Å²
3-	-	-	-1.959 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→41.975 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3774	0	23	144	3941

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	3929
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	3419
X-RAY DIFFRACTION	r_angle_refined_deg	1.318	1.653	5356
X-RAY DIFFRACTION	r_angle_other_deg	1.149	1.58	7963
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.424	5	469
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.837	23.045	220
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.509	15	617
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.103	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.047	0.2	484
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4430
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	879
X-RAY DIFFRACTION	r_nbd_refined	0.179	0.2	691
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.176	0.2	3368
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	1812
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	1720
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	209
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.137	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.186	0.2	25
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.102	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	1.085	3.662	1861
X-RAY DIFFRACTION	r_mcbond_other	1.085	3.662	1860
X-RAY DIFFRACTION	r_mcangle_it	1.784	5.49	2326
X-RAY DIFFRACTION	r_mcangle_other	1.784	5.49	2327
X-RAY DIFFRACTION	r_scbond_it	1.123	3.8	2068
X-RAY DIFFRACTION	r_scbond_other	1.123	3.8	2068
X-RAY DIFFRACTION	r_scangle_it	1.826	5.659	3027
X-RAY DIFFRACTION	r_scangle_other	1.826	5.66	3028
X-RAY DIFFRACTION	r_lrange_it	3.689	41.569	4363
X-RAY DIFFRACTION	r_lrange_other	3.637	41.399	4333

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	0.321	138	0.318	2761	X-RAY DIFFRACTION	93.2454
2.001-2.055	0.314	151	0.335	2872	X-RAY DIFFRACTION	99.9009
2.055-2.115	0.362	133	0.317	2842	X-RAY DIFFRACTION	99.9328
2.115-2.18	0.349	126	0.294	2625	X-RAY DIFFRACTION	96.3235
2.18-2.251	0.6	113	0.584	2126	X-RAY DIFFRACTION	80.5975
2.251-2.33	0.37	96	0.388	1913	X-RAY DIFFRACTION	74.9627
2.33-2.418	0.274	138	0.235	2441	X-RAY DIFFRACTION	98.888
2.418-2.517	0.293	121	0.213	2369	X-RAY DIFFRACTION	99.6399
2.517-2.629	0.277	120	0.215	2299	X-RAY DIFFRACTION	99.7937
2.629-2.757	0.256	125	0.222	2171	X-RAY DIFFRACTION	99.437
2.757-2.906	0.232	103	0.216	2075	X-RAY DIFFRACTION	99.4067
2.906-3.082	0.261	102	0.208	1965	X-RAY DIFFRACTION	99.375
3.082-3.294	0.21	103	0.209	1846	X-RAY DIFFRACTION	99.3374
3.294-3.557	0.22	90	0.203	1712	X-RAY DIFFRACTION	98.0414
3.557-3.896	0.253	90	0.206	1594	X-RAY DIFFRACTION	98.8843
3.896-4.354	0.187	79	0.152	1445	X-RAY DIFFRACTION	99.1542
4.354-5.025	0.165	74	0.122	1291	X-RAY DIFFRACTION	99.635
5.025-6.148	0.182	59	0.147	1099	X-RAY DIFFRACTION	99.8276
6.148-8.665	0.178	46	0.159	888	X-RAY DIFFRACTION	100
8.665-41.975	0.214	25	0.18	512	X-RAY DIFFRACTION	97.8142

Refinement TLS params.

Method: refined / Origin x: 23.012 Å / Origin y: 18.847 Å / Origin z: 12.442 Å

	11	12	13	21	22	23	31	32	33
T	0.1453 Å²	-0.11 Å²	0.0837 Å²	-	0.1024 Å²	-0.0806 Å²	-	-	0.1756 Å²
L	0.6603 °²	0.0119 °²	-0.9505 °²	-	0.7404 °²	0.0131 °²	-	-	1.3946 °²
S	0.1563 Å °	-0.1958 Å °	0.1672 Å °	-0.1148 Å °	0.126 Å °	0.0057 Å °	-0.214 Å °	0.2841 Å °	-0.2824 Å °

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	25 - 488
2	X-RAY DIFFRACTION	1		B	1 - 2

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