PDB-1uyp: The three-dimensional structure of beta-fructosidase (invertase) ...

ID or keywords:

Entry

Database: PDB / ID: 1uyp

Title

The three-dimensional structure of beta-fructosidase (invertase) from Thermotoga maritima

Components

BETA-FRUCTOSIDASE

Keywords

HYDROLASE / INVERTASE / GLYCOSYL HYDROLASE FAMILY 32 / SUCROSE DEGRADATION / BETA-PROPELLER

Function / homology

Function and homology information

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

Biological species

THERMOTOGA MARITIMA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Alberto, F. / Bignon, C. / Sulzenbacher, G. / Henrissat, B. / Czjzek, M.

Citation

Journal: J. Biol. Chem. / Year: 2004
Title: The three-dimensional structure of invertase (beta-fructosidase) from Thermotoga maritima reveals a bimodular arrangement and an evolutionary relationship between retaining and inverting glycosidases.
Authors: Alberto, F. / Bignon, C. / Sulzenbacher, G. / Henrissat, B. / Czjzek, M.

History

Deposition	Mar 2, 2004	Deposition site: PDBE / Processing site: PDBE
Supersession	Mar 22, 2004	ID: 1UTW
Revision 1.0	Mar 22, 2004	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jun 13, 2018	Group: Data collection / Database references / Refinement description Category: citation / diffrn_radiation / refine Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_radiation.pdbx_diffrn_protocol / _refine.pdbx_method_to_determine_struct
Revision 1.4	Apr 9, 2025	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_conn_type / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1uyp.cif.gz	556.4 KB	Display	PDBx/mmCIF format
PDB format	pdb1uyp.ent.gz	457.7 KB	Display	PDB format
PDBx/mmJSON format	1uyp.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/uy/1uyp ftp://data.pdbj.org/pub/pdb/validation_reports/uy/1uyp	HTTPS FTP

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Related structure data

Similar structure data	1w2t-1 1pxc-d 4ha6-d 4z14-3 6pvf-d 4z11-4 6pvg-d 3nne-2 10mh-d 4z13-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: BETA-FRUCTOSIDASE

B: BETA-FRUCTOSIDASE

C: BETA-FRUCTOSIDASE

D: BETA-FRUCTOSIDASE

E: BETA-FRUCTOSIDASE

F: BETA-FRUCTOSIDASE

hetero molecules

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

1

A: BETA-FRUCTOSIDASE

hetero molecules

defined by author&software
50.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: BETA-FRUCTOSIDASE

hetero molecules

defined by author&software
50.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: BETA-FRUCTOSIDASE

hetero molecules

defined by author&software
50.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: BETA-FRUCTOSIDASE

hetero molecules

defined by author&software
50 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: BETA-FRUCTOSIDASE

hetero molecules

defined by author&software
50.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: BETA-FRUCTOSIDASE

hetero molecules

defined by author&software
50.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.480, 114.670, 130.030
Angle α, β, γ (deg.)	90.00, 98.96, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	TYR	TYR	A	A	17 - 28	17 - 28
2	1	ASP	ASP	TYR	TYR	B	B	17 - 28	17 - 28
3	1	ASP	ASP	TYR	TYR	C	C	17 - 28	17 - 28
4	1	ASP	ASP	TYR	TYR	D	D	17 - 28	17 - 28
5	1	ASP	ASP	TYR	TYR	E	E	17 - 28	17 - 28
6	1	ASP	ASP	TYR	TYR	F	F	17 - 28	17 - 28
1	2	PHE	PHE	PRO	PRO	A	A	31 - 39	31 - 39
2	2	PHE	PHE	PRO	PRO	B	B	31 - 39	31 - 39
3	2	PHE	PHE	PRO	PRO	C	C	31 - 39	31 - 39
4	2	PHE	PHE	PRO	PRO	D	D	31 - 39	31 - 39
5	2	PHE	PHE	PRO	PRO	E	E	31 - 39	31 - 39
6	2	PHE	PHE	PRO	PRO	F	F	31 - 39	31 - 39
1	3	ALA	ALA	VAL	VAL	A	A	49 - 55	49 - 55
2	3	ALA	ALA	VAL	VAL	B	B	49 - 55	49 - 55
3	3	ALA	ALA	VAL	VAL	C	C	49 - 55	49 - 55
4	3	ALA	ALA	VAL	VAL	D	D	49 - 55	49 - 55
5	3	ALA	ALA	VAL	VAL	E	E	49 - 55	49 - 55
6	3	ALA	ALA	VAL	VAL	F	F	49 - 55	49 - 55
1	4	VAL	VAL	ASP	ASP	A	A	62 - 68	62 - 68
2	4	VAL	VAL	ASP	ASP	B	B	62 - 68	62 - 68
3	4	VAL	VAL	ASP	ASP	C	C	62 - 68	62 - 68
4	4	VAL	VAL	ASP	ASP	D	D	62 - 68	62 - 68
5	4	VAL	VAL	ASP	ASP	E	E	62 - 68	62 - 68
6	4	VAL	VAL	ASP	ASP	F	F	62 - 68	62 - 68
1	5	SER	SER	MET	MET	A	A	75 - 85	75 - 85
2	5	SER	SER	MET	MET	B	B	75 - 85	75 - 85
3	5	SER	SER	MET	MET	C	C	75 - 85	75 - 85
4	5	SER	SER	MET	MET	D	D	75 - 85	75 - 85
5	5	SER	SER	MET	MET	E	E	75 - 85	75 - 85
6	5	SER	SER	MET	MET	F	F	75 - 85	75 - 85
1	6	VAL	VAL	ASP	ASP	A	A	88 - 94	88 - 94
2	6	VAL	VAL	ASP	ASP	B	B	88 - 94	88 - 94
3	6	VAL	VAL	ASP	ASP	C	C	88 - 94	88 - 94
4	6	VAL	VAL	ASP	ASP	D	D	88 - 94	88 - 94
5	6	VAL	VAL	ASP	ASP	E	E	88 - 94	88 - 94
6	6	VAL	VAL	ASP	ASP	F	F	88 - 94	88 - 94
1	7	CYS	CYS	LEU	LEU	A	A	106 - 114	106 - 114
2	7	CYS	CYS	LEU	LEU	B	B	106 - 114	106 - 114
3	7	CYS	CYS	LEU	LEU	C	C	106 - 114	106 - 114
4	7	CYS	CYS	LEU	LEU	D	D	106 - 114	106 - 114
5	7	CYS	CYS	LEU	LEU	E	E	106 - 114	106 - 114
6	7	CYS	CYS	LEU	LEU	F	F	106 - 114	106 - 114
1	8	ASP	ASP	THR	THR	A	A	120 - 133	120 - 133
2	8	ASP	ASP	THR	THR	B	B	120 - 133	120 - 133
3	8	ASP	ASP	THR	THR	C	C	120 - 133	120 - 133
4	8	ASP	ASP	THR	THR	D	D	120 - 133	120 - 133
5	8	ASP	ASP	THR	THR	E	E	120 - 133	120 - 133
6	8	ASP	ASP	THR	THR	F	F	120 - 133	120 - 133
1	9	ARG	ARG	TRP	TRP	A	A	137 - 148	137 - 148
2	9	ARG	ARG	TRP	TRP	B	B	137 - 148	137 - 148
3	9	ARG	ARG	TRP	TRP	C	C	137 - 148	137 - 148
4	9	ARG	ARG	TRP	TRP	D	D	137 - 148	137 - 148
5	9	ARG	ARG	TRP	TRP	E	E	137 - 148	137 - 148
6	9	ARG	ARG	TRP	TRP	F	F	137 - 148	137 - 148
1	10	VAL	VAL	ILE	ILE	A	A	151 - 160	151 - 160
2	10	VAL	VAL	ILE	ILE	B	B	151 - 160	151 - 160
3	10	VAL	VAL	ILE	ILE	C	C	151 - 160	151 - 160
4	10	VAL	VAL	ILE	ILE	D	D	151 - 160	151 - 160
5	10	VAL	VAL	ILE	ILE	E	E	151 - 160	151 - 160
6	10	VAL	VAL	ILE	ILE	F	F	151 - 160	151 - 160
1	11	LEU	LEU	PHE	PHE	A	A	164 - 172	164 - 172
2	11	LEU	LEU	PHE	PHE	B	B	164 - 172	164 - 172
3	11	LEU	LEU	PHE	PHE	C	C	164 - 172	164 - 172
4	11	LEU	LEU	PHE	PHE	D	D	164 - 172	164 - 172
5	11	LEU	LEU	PHE	PHE	E	E	164 - 172	164 - 172
6	11	LEU	LEU	PHE	PHE	F	F	164 - 172	164 - 172
1	12	GLY	GLY	LYS	LYS	A	A	178 - 187	178 - 187
2	12	GLY	GLY	LYS	LYS	B	B	178 - 187	178 - 187
3	12	GLY	GLY	LYS	LYS	C	C	178 - 187	178 - 187
4	12	GLY	GLY	LYS	LYS	D	D	178 - 187	178 - 187
5	12	GLY	GLY	LYS	LYS	E	E	178 - 187	178 - 187
6	12	GLY	GLY	LYS	LYS	F	F	178 - 187	178 - 187
1	13	LEU	LEU	ASP	ASP	A	A	194 - 201	194 - 201
2	13	LEU	LEU	ASP	ASP	B	B	194 - 201	194 - 201
3	13	LEU	LEU	ASP	ASP	C	C	194 - 201	194 - 201
4	13	LEU	LEU	ASP	ASP	D	D	194 - 201	194 - 201
5	13	LEU	LEU	ASP	ASP	E	E	194 - 201	194 - 201
6	13	LEU	LEU	ASP	ASP	F	F	194 - 201	194 - 201
1	14	ILE	ILE	ASN	ASN	A	A	204 - 211	204 - 211
2	14	ILE	ILE	ASN	ASN	B	B	204 - 211	204 - 211
3	14	ILE	ILE	ASN	ASN	C	C	204 - 211	204 - 211
4	14	ILE	ILE	ASN	ASN	D	D	204 - 211	204 - 211
5	14	ILE	ILE	ASN	ASN	E	E	204 - 211	204 - 211
6	14	ILE	ILE	ASN	ASN	F	F	204 - 211	204 - 211
1	15	SER	SER	LYS	LYS	A	A	216 - 224	216 - 224
2	15	SER	SER	LYS	LYS	B	B	216 - 224	216 - 224
3	15	SER	SER	LYS	LYS	C	C	216 - 224	216 - 224
4	15	SER	SER	LYS	LYS	D	D	216 - 224	216 - 224
5	15	SER	SER	LYS	LYS	E	E	216 - 224	216 - 224
6	15	SER	SER	LYS	LYS	F	F	216 - 224	216 - 224
1	16	LYS	LYS	GLY	GLY	A	A	229 - 236	229 - 236
2	16	LYS	LYS	GLY	GLY	B	B	229 - 236	229 - 236
3	16	LYS	LYS	GLY	GLY	C	C	229 - 236	229 - 236
4	16	LYS	LYS	GLY	GLY	D	D	229 - 236	229 - 236
5	16	LYS	LYS	GLY	GLY	E	E	229 - 236	229 - 236
6	16	LYS	LYS	GLY	GLY	F	F	229 - 236	229 - 236
1	17	THR	THR	THR	THR	A	A	244 - 248	244 - 248
2	17	THR	THR	THR	THR	B	B	244 - 248	244 - 248
3	17	THR	THR	THR	THR	C	C	244 - 248	244 - 248
4	17	THR	THR	THR	THR	D	D	244 - 248	244 - 248
5	17	THR	THR	THR	THR	E	E	244 - 248	244 - 248
6	17	THR	THR	THR	THR	F	F	244 - 248	244 - 248
1	18	GLY	GLY	TRP	TRP	A	A	255 - 260	255 - 260
2	18	GLY	GLY	TRP	TRP	B	B	255 - 260	255 - 260
3	18	GLY	GLY	TRP	TRP	C	C	255 - 260	255 - 260
4	18	GLY	GLY	TRP	TRP	D	D	255 - 260	255 - 260
5	18	GLY	GLY	TRP	TRP	E	E	255 - 260	255 - 260
6	18	GLY	GLY	TRP	TRP	F	F	255 - 260	255 - 260
1	19	VAL	VAL	LEU	LEU	A	A	285 - 290	285 - 290
2	19	VAL	VAL	LEU	LEU	B	B	285 - 290	285 - 290
3	19	VAL	VAL	LEU	LEU	C	C	285 - 290	285 - 290
4	19	VAL	VAL	LEU	LEU	D	D	285 - 290	285 - 290
5	19	VAL	VAL	LEU	LEU	E	E	285 - 290	285 - 290
6	19	VAL	VAL	LEU	LEU	F	F	285 - 290	285 - 290
1	20	LYS	LYS	LEU	LEU	A	A	293 - 298	293 - 298
2	20	LYS	LYS	LEU	LEU	B	B	293 - 298	293 - 298
3	20	LYS	LYS	LEU	LEU	C	C	293 - 298	293 - 298
4	20	LYS	LYS	LEU	LEU	D	D	293 - 298	293 - 298
5	20	LYS	LYS	LEU	LEU	E	E	293 - 298	293 - 298
6	20	LYS	LYS	LEU	LEU	F	F	293 - 298	293 - 298
1	21	VAL	VAL	GLY	GLY	A	A	306 - 313	306 - 313
2	21	VAL	VAL	GLY	GLY	B	B	306 - 313	306 - 313
3	21	VAL	VAL	GLY	GLY	C	C	306 - 313	306 - 313
4	21	VAL	VAL	GLY	GLY	D	D	306 - 313	306 - 313
5	21	VAL	VAL	GLY	GLY	E	E	306 - 313	306 - 313
6	21	VAL	VAL	GLY	GLY	F	F	306 - 313	306 - 313
1	22	LEU	LEU	LYS	LYS	A	A	317 - 320	317 - 320
2	22	LEU	LEU	LYS	LYS	B	B	317 - 320	317 - 320
3	22	LEU	LEU	LYS	LYS	C	C	317 - 320	317 - 320
4	22	LEU	LEU	LYS	LYS	D	D	317 - 320	317 - 320
5	22	LEU	LEU	LYS	LYS	E	E	317 - 320	317 - 320
6	22	LEU	LEU	LYS	LYS	F	F	317 - 320	317 - 320
1	23	CYS	CYS	GLU	GLU	A	A	328 - 343	328 - 343
2	23	CYS	CYS	GLU	GLU	B	B	328 - 343	328 - 343
3	23	CYS	CYS	GLU	GLU	C	C	328 - 343	328 - 343
4	23	CYS	CYS	GLU	GLU	D	D	328 - 343	328 - 343
5	23	CYS	CYS	GLU	GLU	E	E	328 - 343	328 - 343
6	23	CYS	CYS	GLU	GLU	F	F	328 - 343	328 - 343
1	24	THR	THR	LEU	LEU	A	A	348 - 354	348 - 354
2	24	THR	THR	LEU	LEU	B	B	348 - 354	348 - 354
3	24	THR	THR	LEU	LEU	C	C	348 - 354	348 - 354
4	24	THR	THR	LEU	LEU	D	D	348 - 354	348 - 354
5	24	THR	THR	LEU	LEU	E	E	348 - 354	348 - 354
6	24	THR	THR	LEU	LEU	F	F	348 - 354	348 - 354
1	25	ASP	ASP	SER	SER	A	A	357 - 361	357 - 361
2	25	ASP	ASP	SER	SER	B	B	357 - 361	357 - 361
3	25	ASP	ASP	SER	SER	C	C	357 - 361	357 - 361
4	25	ASP	ASP	SER	SER	D	D	357 - 361	357 - 361
5	25	ASP	ASP	SER	SER	E	E	357 - 361	357 - 361
6	25	ASP	ASP	SER	SER	F	F	357 - 361	357 - 361
1	26	GLY	GLY	GLU	GLU	A	A	362 - 376	362 - 376
2	26	GLY	GLY	GLU	GLU	B	B	362 - 376	362 - 376
3	26	GLY	GLY	GLU	GLU	C	C	362 - 376	362 - 376
4	26	GLY	GLY	GLU	GLU	D	D	362 - 376	362 - 376
5	26	GLY	GLY	GLU	GLU	E	E	362 - 376	362 - 376
6	26	GLY	GLY	GLU	GLU	F	F	362 - 376	362 - 376
1	27	ASP	ASP	VAL	VAL	A	A	386 - 390	386 - 390
2	27	ASP	ASP	VAL	VAL	B	B	386 - 390	386 - 390
3	27	ASP	ASP	VAL	VAL	C	C	386 - 390	386 - 390
4	27	ASP	ASP	VAL	VAL	D	D	386 - 390	386 - 390
5	27	ASP	ASP	VAL	VAL	E	E	386 - 390	386 - 390
6	27	ASP	ASP	VAL	VAL	F	F	386 - 390	386 - 390
1	28	PHE	PHE	ILE	ILE	A	A	393 - 398	393 - 398
2	28	PHE	PHE	ILE	ILE	B	B	393 - 398	393 - 398
3	28	PHE	PHE	ILE	ILE	C	C	393 - 398	393 - 398
4	28	PHE	PHE	ILE	ILE	D	D	393 - 398	393 - 398
5	28	PHE	PHE	ILE	ILE	E	E	393 - 398	393 - 398
6	28	PHE	PHE	ILE	ILE	F	F	393 - 398	393 - 398
1	29	PHE	PHE	GLU	GLU	A	A	402 - 407	402 - 407
2	29	PHE	PHE	GLU	GLU	B	B	402 - 407	402 - 407
3	29	PHE	PHE	GLU	GLU	C	C	402 - 407	402 - 407
4	29	PHE	PHE	GLU	GLU	D	D	402 - 407	402 - 407
5	29	PHE	PHE	GLU	GLU	E	E	402 - 407	402 - 407
6	29	PHE	PHE	GLU	GLU	F	F	402 - 407	402 - 407
1	30	LYS	LYS	LEU	LEU	A	A	416 - 432	416 - 432
2	30	LYS	LYS	LEU	LEU	B	B	416 - 432	416 - 432
3	30	LYS	LYS	LEU	LEU	C	C	416 - 432	416 - 432
4	30	LYS	LYS	LEU	LEU	D	D	416 - 432	416 - 432
5	30	LYS	LYS	LEU	LEU	E	E	416 - 432	416 - 432
6	30	LYS	LYS	LEU	LEU	F	F	416 - 432	416 - 432

NCS oper:

ID	Code	Matrix	Vector
1	given	(1, -0.000162, 0.000216), (0.000162, 1, -9.5E-5), (-0.000216, 9.5E-5, 1)	-0.01542, 0.00795, 0.00113
2	given	(1, 0.000225, 0.000693), (-0.000226, 1, 0.000365), (-0.000693, -0.000365, 1)	-0.01318, -0.01009, 0.00019
3	given	(1, -7.8E-5, -2.8E-5), (7.8E-5, 1, -0.00014), (2.8E-5, 0.00014, 1)	-0.00112, -0.00564, -0.00032
4	given	(1, 0.000842, 0.000187), (-0.000842, 1, 0.000408), (-0.000186, -0.000408, 1)	0.01214, -0.00274, -0.0048
5	given	(1, -8.4E-5, -0.000585), (8.5E-5, 1, 0.000412), (0.000585, -0.000412, 1)	-0.03445, 0.02662, 0.0063

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	BETA-FRUCTOSIDASE Mass: 49886.191 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM 3109) / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O33833, beta-fructofuranosidase

#1: Protein

BETA-FRUCTOSIDASE

Mass: 49886.191 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM 3109) / Plasmid: PDEST17 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O33833, beta-fructofuranosidase

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Non-polymers , 5 types, 1778 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1756 / Source method: isolated from a natural source / Formula: H₂O

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Details

Compound details	CATALYSES HYDROLYSIS OF TERMINAL NON-REDUCING BETA-D- FRUCTOFURANOSIDE RESIDUES IN BETA-D-FRUCTOFURANOSIDES.
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: 2.2 Å³/Da / Density % sol: 43 %

Crystal grow

pH: 4.2
Details: 15 % PEG 1000, 150 MM LI2SO4, 100 MM CITRATE PHOSPHATE BUFFER PH 4.2

Crystal grow

*PLUS

Temperature: 20 ℃ / pH: 4.2 / Method: vapor diffusion

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Chemical formula	Details
1	15 %	PEG1000	1	drop
2	150 mM		1	drop	Li2SO4
3	100 mM	sodium citrate	1	drop		pH4.2
4	11 mg/ml	protein	1	drop
5	17 %	PEG1000	1	reservoir
6	50 mM		1	reservoir	Li2SO4
7	1 %	isopropanol	1	reservoir
8	100 mM	sodium citrate	1	reservoir		pH4.2

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Data collection

Diffraction	Mean temperature: 197 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792
Detector	Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2003 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.9→34 Å / Num. obs: 184592 / % possible obs: 99.9 % / Redundancy: 3.1 % / R_merge(I) obs: 0.083 / Net I/σ(I): 6.5
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 1.9 / % possible all: 100
Reflection	PLUS Highest resolution: 2 Å / Redundancy: 3.1 % / R_merge(I) obs*: 0.077
Reflection shell	PLUS % possible obs: 99.9 % / Redundancy: 3.1 % / R_merge(I) obs: 0.402 / Mean I/σ(I) obs*: 2.1

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
MOSFLM		data reduction
SCALA		data scaling
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.9→129.1 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.934 / SU B: 2.695 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22	10694	5 %	RANDOM
R_work	0.177	-	-	-
obs	0.179	202520	99.1 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 23.82 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.4 Å²	0 Å²	0.92 Å²
2-	-	-0.11 Å²	0 Å²
3-	-	-	-1 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→129.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21120	0	120	1756	22996

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.021	21764
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	19114
X-RAY DIFFRACTION	r_angle_refined_deg	1.742	1.945	29453
X-RAY DIFFRACTION	r_angle_other_deg	1.001	3	44578
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.448	5	2586
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.137	0.2	3096
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	24126
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	4632
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	3925
X-RAY DIFFRACTION	r_nbd_other	0.263	0.2	23750
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.094	0.2	13481
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.195	0.2	1306
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.349	0.2	2
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.268	0.2	77
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.293	0.2	250
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.184	0.2	66
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.968	1.5	12864
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.868	2	20850
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.815	3	8900
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.588	4.5	8603
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1538	tight positional	0.09	0.05
2	B	1538	tight positional	0.07	0.05
3	C	1538	tight positional	0.07	0.05
4	D	1538	tight positional	0.07	0.05
5	E	1538	tight positional	0.06	0.05
6	F	1538	tight positional	0.08	0.05
1	A	2395	loose positional	0.54	5
2	B	2395	loose positional	0.6	5
3	C	2395	loose positional	0.66	5
4	D	2395	loose positional	0.48	5
5	E	2395	loose positional	0.49	5
6	F	2395	loose positional	0.63	5
1	A	1538	tight thermal	0.2	0.5
2	B	1538	tight thermal	0.17	0.5
3	C	1538	tight thermal	0.19	0.5
4	D	1538	tight thermal	0.17	0.5
5	E	1538	tight thermal	0.16	0.5
6	F	1538	tight thermal	0.18	0.5
1	A	2395	loose thermal	1.69	10
2	B	2395	loose thermal	1.5	10
3	C	2395	loose thermal	1.62	10
4	D	2395	loose thermal	1.38	10
5	E	2395	loose thermal	1.54	10
6	F	2395	loose thermal	1.47	10

LS refinement shell

Resolution: 1.9→1.95 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.296	706
R_work	0.27	13649

Refinement

*PLUS

% reflection R_free: 5 % / R_factor R_work: 0.176

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.027
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	2.24

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