PDB-3wq8: Monomer structure of hyperthermophilic beta-glucosidase mutant fo...

Basic information

• Entry: Database: PDB / ID: 3wq8
• Title: Monomer structure of hyperthermophilic beta-glucosidase mutant forming a dodecameric structure in the crystal form
• Components: Beta-glucosidase
• Keywords: HYDROLASE / TIM BARREL / SUGAR BINDING / HYDROLYSIS

Function / homology

Function:

beta-glucosidase activity / carbohydrate metabolic process

Domain/homology:

: / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta

Component:

Beta-galactosidase

• Biological species: Pyrococcus furiosus (archaea)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
• Authors: Nakabayashi, M. / Kataoka, M. / Watanabe, M. / Ishikawa, K.
• Citation: Journal: Acta Crystallogr.,Sect.F / Year: 2014; Title: Monomer structure of a hyperthermophilic beta-glucosidase mutant forming a dodecameric structure in the crystal form.; Authors: Nakabayashi, M. / Kataoka, M. / Watanabe, M. / Ishikawa, K.

History

Deposition	Jan 23, 2014	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 9, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2019	Group: Database references / Category: citation / struct_ref_seq_dif Item: _citation.country / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Assembly

Deposited unit

A: Beta-glucosidase

B: Beta-glucosidase

C: Beta-glucosidase

D: Beta-glucosidase

E: Beta-glucosidase

F: Beta-glucosidase

G: Beta-glucosidase

H: Beta-glucosidase

I: Beta-glucosidase

J: Beta-glucosidase

K: Beta-glucosidase

L: Beta-glucosidase

Summary:

• 622 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	622,340	12
Polymers	622,340	12
Non-polymers	0	0
Water	2,270	126

1

A: Beta-glucosidase

Summary:

• defined by author&software
• 51.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	51,862	1
Polymers	51,862	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

2

B: Beta-glucosidase

Summary:

• defined by author&software
• 51.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	51,862	1
Polymers	51,862	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

3

C: Beta-glucosidase

Summary:

• defined by author&software
• 51.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	51,862	1
Polymers	51,862	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

4

D: Beta-glucosidase

Summary:

• defined by author&software
• 51.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	51,862	1
Polymers	51,862	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

5

E: Beta-glucosidase

Summary:

• defined by author&software
• 51.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	51,862	1
Polymers	51,862	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

6

F: Beta-glucosidase

Summary:

• defined by author&software
• 51.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	51,862	1
Polymers	51,862	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

7

G: Beta-glucosidase

Summary:

• defined by author&software
• 51.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	51,862	1
Polymers	51,862	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

8

H: Beta-glucosidase

Summary:

• defined by author&software
• 51.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	51,862	1
Polymers	51,862	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

9

I: Beta-glucosidase

Summary:

• defined by author&software
• 51.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	51,862	1
Polymers	51,862	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

10

J: Beta-glucosidase

Summary:

• defined by author&software
• 51.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	51,862	1
Polymers	51,862	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

11

K: Beta-glucosidase

Summary:

• defined by author&software
• 51.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	51,862	1
Polymers	51,862	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

12

L: Beta-glucosidase

Summary:

• defined by author&software
• 51.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	51,862	1
Polymers	51,862	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

Unit cell

Length a, b, c (Å)	97.365, 148.872, 148.563
Angle α, β, γ (deg.)	120.08, 94.00, 99.70
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	A
2	10	K
1	11	A
2	11	L
1	12	B
2	12	C
1	13	B
2	13	D
1	14	B
2	14	E
1	15	B
2	15	F
1	16	B
2	16	G
1	17	B
2	17	H
1	18	B
2	18	I
1	19	B
2	19	J
1	20	B
2	20	K
1	21	B
2	21	L
1	22	C
2	22	D
1	23	C
2	23	E
1	24	C
2	24	F
1	25	C
2	25	G
1	26	C
2	26	H
1	27	C
2	27	I
1	28	C
2	28	J
1	29	C
2	29	K
1	30	C
2	30	L
1	31	D
2	31	E
1	32	D
2	32	F
1	33	D
2	33	G
1	34	D
2	34	H
1	35	D
2	35	I
1	36	D
2	36	J
1	37	D
2	37	K
1	38	D
2	38	L
1	39	E
2	39	F
1	40	E
2	40	G
1	41	E
2	41	H
1	42	E
2	42	I
1	43	E
2	43	J
1	44	E
2	44	K
1	45	E
2	45	L
1	46	F
2	46	G
1	47	F
2	47	H
1	48	F
2	48	I
1	49	F
2	49	J
1	50	F
2	50	K
1	51	F
2	51	L
1	52	G
2	52	H
1	53	G
2	53	I
1	54	G
2	54	J
1	55	G
2	55	K
1	56	G
2	56	L
1	57	H
2	57	I
1	58	H
2	58	J
1	59	H
2	59	K
1	60	H
2	60	L
1	61	I
2	61	J
1	62	I
2	62	K
1	63	I
2	63	L
1	64	J
2	64	K
1	65	J
2	65	L
1	66	K
2	66	L

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 2 - 449 / Label seq-ID: 3 - 450

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	A	A
2	8	I	I
1	9	A	A
2	9	J	J
1	10	A	A
2	10	K	K
1	11	A	A
2	11	L	L
1	12	B	B
2	12	C	C
1	13	B	B
2	13	D	D
1	14	B	B
2	14	E	E
1	15	B	B
2	15	F	F
1	16	B	B
2	16	G	G
1	17	B	B
2	17	H	H
1	18	B	B
2	18	I	I
1	19	B	B
2	19	J	J
1	20	B	B
2	20	K	K
1	21	B	B
2	21	L	L
1	22	C	C
2	22	D	D
1	23	C	C
2	23	E	E
1	24	C	C
2	24	F	F
1	25	C	C
2	25	G	G
1	26	C	C
2	26	H	H
1	27	C	C
2	27	I	I
1	28	C	C
2	28	J	J
1	29	C	C
2	29	K	K
1	30	C	C
2	30	L	L
1	31	D	D
2	31	E	E
1	32	D	D
2	32	F	F
1	33	D	D
2	33	G	G
1	34	D	D
2	34	H	H
1	35	D	D
2	35	I	I
1	36	D	D
2	36	J	J
1	37	D	D
2	37	K	K
1	38	D	D
2	38	L	L
1	39	E	E
2	39	F	F
1	40	E	E
2	40	G	G
1	41	E	E
2	41	H	H
1	42	E	E
2	42	I	I
1	43	E	E
2	43	J	J
1	44	E	E
2	44	K	K
1	45	E	E
2	45	L	L
1	46	F	F
2	46	G	G
1	47	F	F
2	47	H	H
1	48	F	F
2	48	I	I
1	49	F	F
2	49	J	J
1	50	F	F
2	50	K	K
1	51	F	F
2	51	L	L
1	52	G	G
2	52	H	H
1	53	G	G
2	53	I	I
1	54	G	G
2	54	J	J
1	55	G	G
2	55	K	K
1	56	G	G
2	56	L	L
1	57	H	H
2	57	I	I
1	58	H	H
2	58	J	J
1	59	H	H
2	59	K	K
1	60	H	H
2	60	L	L
1	61	I	I
2	61	J	J
1	62	I	I
2	62	K	K
1	63	I	I
2	63	L	L
1	64	J	J
2	64	K	K
1	65	J	J
2	65	L	L
1	66	K	K
2	66	L	L

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

Components

#1: Protein

A B C D E F G H I J K L
Beta-glucosidase

Details:

Mass: 51861.664 Da / Num. of mol.: 12 / Fragment: UNP residues 2-446 / Mutation: R170A, R220A, Y227F, F447S, R448V, E449K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: celB / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q51723, beta-glucosidase

#2: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.9 ų/Da / Density % sol: 57.63 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 ; Details: 0.1M HEPES-NaOH pH7.6, 0.2M Ca-Acetate, 20% PEG 3350, 5% Ethyleneglycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
• Detector: Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 1, 2013
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9 Å / Relative weight: 1
• Reflection: Resolution: 2.81→48.28 Å / Num. obs: 170856 / R_merge(I) obs: 0.11 / Net I/σ(I): 28.7

Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WDP

3wdp

Resolution: 2.81→48.28 Å / Cor.coef. F_o:F_c: 0.888 / Cor.coef. F_o:F_c free: 0.855 / SU B: 18.046 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.27497	8298	5 %	RANDOM
Rwork	0.24299	-	-	-
obs	0.2446	156940	96.44 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 61.032 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-2.38 Å2	-0.43 Å2	0.01 Å2
2-	-	0.59 Å2	0.3 Å2
3-	-	-	0.91 Å2

Refinement step

Cycle: LAST / Resolution: 2.81→48.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	43636	0	0	126	43762

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	45060
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	41308
X-RAY DIFFRACTION	r_angle_refined_deg	1.48	1.94	61152
X-RAY DIFFRACTION	r_angle_other_deg	1.444	3	95272
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.106	5	5324
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.664	23.95	2228
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.414	15	7296
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.752	15	192
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	6120
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	50892
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	10884
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	28666	0.06
1	2	B	28666	0.06
2	1	A	28745	0.05
2	2	C	28745	0.05
3	1	A	28425	0.07
3	2	D	28425	0.07
4	1	A	28685	0.06
4	2	E	28685	0.06
5	1	A	28459	0.07
5	2	F	28459	0.07
6	1	A	29002	0.06
6	2	G	29002	0.06
7	1	A	28775	0.07
7	2	H	28775	0.07
8	1	A	28845	0.05
8	2	I	28845	0.05
9	1	A	28304	0.07
9	2	J	28304	0.07
10	1	A	28828	0.06
10	2	K	28828	0.06
11	1	A	28779	0.06
11	2	L	28779	0.06
12	1	B	28700	0.06
12	2	C	28700	0.06
13	1	B	28609	0.07
13	2	D	28609	0.07
14	1	B	28665	0.06
14	2	E	28665	0.06
15	1	B	28518	0.07
15	2	F	28518	0.07
16	1	B	28566	0.06
16	2	G	28566	0.06
17	1	B	28671	0.06
17	2	H	28671	0.06
18	1	B	28812	0.06
18	2	I	28812	0.06
19	1	B	28367	0.07
19	2	J	28367	0.07
20	1	B	28723	0.06
20	2	K	28723	0.06
21	1	B	28463	0.06
21	2	L	28463	0.06
22	1	C	28587	0.07
22	2	D	28587	0.07
23	1	C	28657	0.06
23	2	E	28657	0.06
24	1	C	28498	0.07
24	2	F	28498	0.07
25	1	C	28689	0.06
25	2	G	28689	0.06
26	1	C	28487	0.07
26	2	H	28487	0.07
27	1	C	28899	0.05
27	2	I	28899	0.05
28	1	C	28413	0.07
28	2	J	28413	0.07
29	1	C	28749	0.06
29	2	K	28749	0.06
30	1	C	28579	0.06
30	2	L	28579	0.06
31	1	D	28487	0.07
31	2	E	28487	0.07
32	1	D	28592	0.07
32	2	F	28592	0.07
33	1	D	28392	0.07
33	2	G	28392	0.07
34	1	D	28418	0.07
34	2	H	28418	0.07
35	1	D	28632	0.07
35	2	I	28632	0.07
36	1	D	28462	0.07
36	2	J	28462	0.07
37	1	D	28510	0.07
37	2	K	28510	0.07
38	1	D	28564	0.06
38	2	L	28564	0.06
39	1	E	28515	0.06
39	2	F	28515	0.06
40	1	E	28559	0.06
40	2	G	28559	0.06
41	1	E	28499	0.07
41	2	H	28499	0.07
42	1	E	28751	0.06
42	2	I	28751	0.06
43	1	E	28270	0.07
43	2	J	28270	0.07
44	1	E	28711	0.06
44	2	K	28711	0.06
45	1	E	28347	0.06
45	2	L	28347	0.06
46	1	F	28447	0.07
46	2	G	28447	0.07
47	1	F	28304	0.07
47	2	H	28304	0.07
48	1	F	28543	0.07
48	2	I	28543	0.07
49	1	F	28532	0.06
49	2	J	28532	0.06
50	1	F	28511	0.07
50	2	K	28511	0.07
51	1	F	28491	0.06
51	2	L	28491	0.06
52	1	G	28635	0.07
52	2	H	28635	0.07
53	1	G	28701	0.06
53	2	I	28701	0.06
54	1	G	28263	0.07
54	2	J	28263	0.07
55	1	G	28743	0.06
55	2	K	28743	0.06
56	1	G	28771	0.06
56	2	L	28771	0.06
57	1	H	28640	0.06
57	2	I	28640	0.06
58	1	H	28176	0.08
58	2	J	28176	0.08
59	1	H	28603	0.07
59	2	K	28603	0.07
60	1	H	28601	0.07
60	2	L	28601	0.07
61	1	I	28461	0.07
61	2	J	28461	0.07
62	1	I	28842	0.05
62	2	K	28842	0.05
63	1	I	28604	0.06
63	2	L	28604	0.06
64	1	J	28325	0.07
64	2	K	28325	0.07
65	1	J	28398	0.06
65	2	L	28398	0.06
66	1	K	28549	0.06
66	2	L	28549	0.06

LS refinement shell

Resolution: 2.805→2.903 Å / Total num. of bins used: 15

	Rfactor	Num. reflection	% reflection
Rfree	0.389	734	-
Rwork	0.342	14270	-
obs	-	-	89.69 %