PDB-4d1j: The structure of the GH35 beta-galactosidase Bgl35A from Cellvibr...

ID or keywords:

Entry

Database: PDB / ID: 4d1j

Title

The structure of the GH35 beta-galactosidase Bgl35A from Cellvibrio japonicas in complex with 1-Deoxygalactonojirimycin

Components

BETA-GALACTOSIDASE, PUTATIVE, BGL35A

Keywords

HYDROLASE / ENZYME-CARBOHYDRATE INTERACTION / GLYCOSIDASE INHIBITION

Function / homology

Function and homology information

beta-galactosidase complex /

beta-galactosidase /

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

Biological species

CELLVIBRIO JAPONICUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Larsbrink, J. / Thompson, A.J. / Lundqvist, M. / Gardner, J.G. / Davies, G.J. / Brumer, H.

Citation

Journal: Mol.Microbiol. / Year: 2014
Title: A Complex Gene Locus Enables Xyloglucan Utilization in the Model Saprophyte Cellvibrio Japonicus.
Authors: Larsbrink, J. / Thompson, A.J. / Lundqvist, M. / Gardner, J.G. / Davies, G.J. / Brumer, H.

History

Deposition	May 2, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 28, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 22, 2014	Group: Database references
Revision 1.2	Mar 11, 2020	Group: Derived calculations / Other Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4d1j.cif.gz	916.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4d1j.ent.gz	752.9 KB	Display	PDB format
PDBx/mmJSON format	4d1j.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/d1/4d1j ftp://data.pdbj.org/pub/pdb/validation_reports/d1/4d1j	HTTPS FTP

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Related structure data

Related structure data	4d1iC 3u7vS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5jaw-1 6tbk-6 6tbh-5 6tbi-2 5upl-d 6tbf-5 6tbg-8 1w69-1 6tbg-5 5jaw-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) 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) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

B: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

C: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

D: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

E: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

F: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

G: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

H: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

hetero molecules

490 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

B: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

C: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

H: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

hetero molecules

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

2

D: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

E: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

F: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

G: BETA-GALACTOSIDASE, PUTATIVE, BGL35A

hetero molecules

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

Unit cell

Length a, b, c (Å)	99.257, 116.095, 116.113
Angle α, β, γ (deg.)	90.00, 90.05, 90.04
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 0

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLN	GLN	A	A	37 - 575	2 - 540
2	1	GLN	GLN	B	B	37 - 575	2 - 540
1	2	GLN	GLN	A	A	37 - 575	2 - 540
2	2	GLN	GLN	C	C	37 - 575	2 - 540
1	3	VAL	VAL	A	A	37 - 574	2 - 539
2	3	VAL	VAL	D	D	37 - 574	2 - 539
1	4	GLN	GLN	A	A	37 - 575	2 - 540
2	4	GLN	GLN	E	E	37 - 575	2 - 540
1	5	GLN	GLN	A	A	37 - 575	2 - 540
2	5	GLN	GLN	F	F	37 - 575	2 - 540
1	6	VAL	VAL	A	A	37 - 574	2 - 539
2	6	VAL	VAL	G	G	37 - 574	2 - 539
1	7	GLN	GLN	A	A	37 - 575	2 - 540
2	7	GLN	GLN	H	H	37 - 575	2 - 540
1	8	GLN	GLN	B	B	37 - 575	2 - 540
2	8	GLN	GLN	C	C	37 - 575	2 - 540
1	9	VAL	VAL	B	B	37 - 574	2 - 539
2	9	VAL	VAL	D	D	37 - 574	2 - 539
1	10	GLN	GLN	B	B	37 - 575	2 - 540
2	10	GLN	GLN	E	E	37 - 575	2 - 540
1	11	GLN	GLN	B	B	37 - 575	2 - 540
2	11	GLN	GLN	F	F	37 - 575	2 - 540
1	12	VAL	VAL	B	B	37 - 574	2 - 539
2	12	VAL	VAL	G	G	37 - 574	2 - 539
1	13	GLN	GLN	B	B	37 - 575	2 - 540
2	13	GLN	GLN	H	H	37 - 575	2 - 540
1	14	VAL	VAL	C	C	37 - 574	2 - 539
2	14	VAL	VAL	D	D	37 - 574	2 - 539
1	15	GLN	GLN	C	C	37 - 575	2 - 540
2	15	GLN	GLN	E	E	37 - 575	2 - 540
1	16	GLN	GLN	C	C	37 - 575	2 - 540
2	16	GLN	GLN	F	F	37 - 575	2 - 540
1	17	VAL	VAL	C	C	37 - 574	2 - 539
2	17	VAL	VAL	G	G	37 - 574	2 - 539
1	18	GLN	GLN	C	C	37 - 575	2 - 540
2	18	GLN	GLN	H	H	37 - 575	2 - 540
1	19	VAL	VAL	D	D	37 - 574	2 - 539
2	19	VAL	VAL	E	E	37 - 574	2 - 539
1	20	VAL	VAL	D	D	37 - 574	2 - 539
2	20	VAL	VAL	F	F	37 - 574	2 - 539
1	21	GLN	GLN	D	D	36 - 575	1 - 540
2	21	GLN	GLN	G	G	36 - 575	1 - 540
1	22	VAL	VAL	D	D	37 - 574	2 - 539
2	22	VAL	VAL	H	H	37 - 574	2 - 539
1	23	GLN	GLN	E	E	37 - 575	2 - 540
2	23	GLN	GLN	F	F	37 - 575	2 - 540
1	24	VAL	VAL	E	E	37 - 574	2 - 539
2	24	VAL	VAL	G	G	37 - 574	2 - 539
1	25	GLN	GLN	E	E	37 - 575	2 - 540
2	25	GLN	GLN	H	H	37 - 575	2 - 540
1	26	VAL	VAL	F	F	37 - 574	2 - 539
2	26	VAL	VAL	G	G	37 - 574	2 - 539
1	27	GLN	GLN	F	F	37 - 575	2 - 540
2	27	GLN	GLN	H	H	37 - 575	2 - 540
1	28	VAL	VAL	G	G	37 - 574	2 - 539
2	28	VAL	VAL	H	H	37 - 574	2 - 539

NCS ensembles :
NCS oper: (Code: given
Matrix: (0.9985, -0.055, -0.0022), (-0.0022, -1), (0.055, 0.9985, -0.0002)
Vector: 3.5974, -0.7981, -4.5506)

#1: Protein	BETA-GALACTOSIDASE, PUTATIVE, BGL35A / / BGL35A Mass: 60935.723 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Strain: UEDA107 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER / References: UniProt: B3PBE0, beta-galactosidase
#2: Chemical	ChemComp-DGJ / (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol / 1-deoxygalactonojirimycin / Migalastat Mass: 163.172 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄ / Comment: medication, Galafold*YM
#3: Chemical	... ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 4011 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	PROTEIN IS TRUNCATED AT AMINO ACID 36 TO REMOVE N-TERMINAL SIGNAL PEPTIDE

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54.4 % / Description: NONE
Crystal grow	pH: 7 / Details: 2.8 M SODIUM ACETATE PH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 466658 / % possible obs: 97.1 % / Observed criterion σ(I): -3.7 / Redundancy: 2.2 % / B_iso Wilson estimate: 20.1 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 9.8
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.57 / Mean I/σ(I) obs: 1.4 / % possible all: 95.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U7V

3u7v

Resolution: 1.8→116.11 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.959 / SU B: 3.178 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19482	23426	5 %	RANDOM
R_work	0.17169	-	-	-
obs	0.17286	443137	97.08 %	-

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: 28.627 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.4 Å²	0.13 Å²	0.64 Å²
2-	-	-0.35 Å²	0.21 Å²
3-	-	-	-1.05 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→116.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	33387	0	131	4011	37529

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	34694
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	31944
X-RAY DIFFRACTION	r_angle_refined_deg	1.466	1.951	47416
X-RAY DIFFRACTION	r_angle_other_deg	1.272	3	73256
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.608	5	4398
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.442	24.254	1601
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.394	15	5243
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.418	15	194
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	5159
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	40153
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	8157
X-RAY DIFFRACTION	r_nbd_refined	0.271	0.2	11829
X-RAY DIFFRACTION	r_nbd_other	0.183	0.2	30888
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	17226
X-RAY DIFFRACTION	r_nbtor_other	0.088	0.2	15860
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	904
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.135	0.2	26
X-RAY DIFFRACTION	r_metal_ion_refined	0.123	0.2	56
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.308	0.2	195
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.287	0.2	268
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.114	0.2	30
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.073	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.952	2.812	17355
X-RAY DIFFRACTION	r_mcbond_other	1.952	2.812	17353
X-RAY DIFFRACTION	r_mcangle_it	2.814	4.212	21695
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.537	2.89	17339
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.86	4.262	25674
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	32765	0.04
1	2	B	32765	0.04
2	1	A	32391	0.05
2	2	C	32391	0.05
3	1	A	32823	0.04
3	2	D	32823	0.04
4	1	A	32413	0.07
4	2	E	32413	0.07
5	1	A	32248	0.07
5	2	F	32248	0.07
6	1	A	32243	0.07
6	2	G	32243	0.07
7	1	A	31930	0.07
7	2	H	31930	0.07
8	1	B	32269	0.04
8	2	C	32269	0.04
9	1	B	32757	0.04
9	2	D	32757	0.04
10	1	B	32135	0.07
10	2	E	32135	0.07
11	1	B	32083	0.06
11	2	F	32083	0.06
12	1	B	32132	0.07
12	2	G	32132	0.07
13	1	B	31943	0.06
13	2	H	31943	0.06
14	1	C	32597	0.04
14	2	D	32597	0.04
15	1	C	32096	0.06
15	2	E	32096	0.06
16	1	C	32041	0.06
16	2	F	32041	0.06
17	1	C	32073	0.06
17	2	G	32073	0.06
18	1	C	31900	0.06
18	2	H	31900	0.06
19	1	D	32540	0.07
19	2	E	32540	0.07
20	1	D	32473	0.07
20	2	F	32473	0.07
21	1	D	32527	0.07
21	2	G	32527	0.07
22	1	D	32321	0.06
22	2	H	32321	0.06
23	1	E	32211	0.07
23	2	F	32211	0.07
24	1	E	32575	0.06
24	2	G	32575	0.06
25	1	E	32182	0.06
25	2	H	32182	0.06
26	1	F	32457	0.07
26	2	G	32457	0.07
27	1	F	32291	0.06
27	2	H	32291	0.06
28	1	G	32030	0.06
28	2	H	32030	0.06

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.327	1686	-
R_work	0.314	32480	-
obs	-	-	95.57 %

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Mar 5, 2020. Novel coronavirus structure data

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Jul 12, 2017. Major update of PDB

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Yorodumi