PDB-7nit: X-ray structure of a multidomain BbgIII from Bifidobacterium bifidum

ID or keywords:

Entry

Database: PDB / ID: 7nit

Title

X-ray structure of a multidomain BbgIII from Bifidobacterium bifidum

Components

Beta-galactosidase

Keywords

HYDROLASE / Bifidobacterium bifidum / lactose hydrolysis / galactooligosaccharides / transgalactosylation

Function / homology

Function and homology information

hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding / membrane
Similarity search - Function

Biological species

Bifidobacterium bifidum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.89 Å

Authors

Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Sanchez Rodriguez, F. / Rigden, D.J. / Tams, J.W. / Wilting, R. / Vester, J.K. / Longhin, E. / Krogh, K.B.R. ...

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions.
Authors: Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Sanchez Rodriguez, F. / Rigden, D.J. / Tams, J.W. / Wilting, R. / Vester, J.K. / Longhin, E. / Hansen, G.H. / Krogh, K.B.R.M. / Pache, R.A. / ...

History

Deposition	Feb 14, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 22, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7nit.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb7nit.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	7nit.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7nit_validation.pdf.gz	542.1 KB	Display	wwPDB validaton report
Full document	7nit_full_validation.pdf.gz	662.7 KB	Display
Data in XML	7nit_validation.xml.gz	234.3 KB	Display
Data in CIF	7nit_validation.cif.gz	318.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ni/7nit ftp://data.pdbj.org/pub/pdb/validation_reports/ni/7nit	HTTPS FTP

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Related structure data

Related structure data	1gofS 2w1sS 2wdcS 3f2zS 4lplS 5dmyS S: Starting model for refinement
Similar structure data	7nit-3 7nit-4 5dxh-2 7lm2-d 7k5z-d 3zqj-3 3zqj-5 5m6u-d 6o07-d 6xv5-d 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

Related structure data

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (8) #39 - Mar 2003 lac Repressor similarity (8) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (3) #141 - Sep 2011 O-GlcNAc Transferase similarity (2)

Deposited unit

A: Beta-galactosidase

B: Beta-galactosidase

C: Beta-galactosidase

D: Beta-galactosidase

E: Beta-galactosidase

F: Beta-galactosidase

hetero molecules

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

1

A: Beta-galactosidase

hetero molecules

defined by author&software
Evidence: gel filtration
140 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Beta-galactosidase

hetero molecules

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

3

C: Beta-galactosidase

hetero molecules

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

4

D: Beta-galactosidase

hetero molecules

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

5

E: Beta-galactosidase

hetero molecules

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

6

F: Beta-galactosidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	116.947, 130.042, 200.580
Angle α, β, γ (deg.)	86.991, 84.830, 83.788
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-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	1	SER	SER	THR	THR	A	A	15 - 1285	15 - 1285
2	2	1	SER	SER	THR	THR	B	B	15 - 1285	15 - 1285
3	3	2	THR	THR	THR	THR	A	A	11 - 1285	11 - 1285
4	4	2	THR	THR	THR	THR	C	C	11 - 1285	11 - 1285
5	5	3	THR	THR	PHE	PHE	A	A	11 - 1286	11 - 1286
6	6	3	THR	THR	PHE	PHE	D	D	11 - 1286	11 - 1286
7	7	4	SER	SER	THR	THR	A	A	15 - 1285	15 - 1285
8	8	4	SER	SER	THR	THR	E	E	15 - 1285	15 - 1285
9	9	5	THR	THR	THR	THR	A	A	11 - 1285	11 - 1285
10	10	5	THR	THR	THR	THR	F	F	11 - 1285	11 - 1285
11	11	6	SER	SER	THR	THR	B	B	15 - 1285	15 - 1285
12	12	6	SER	SER	THR	THR	C	C	15 - 1285	15 - 1285
13	13	7	SER	SER	PHE	PHE	B	B	15 - 1286	15 - 1286
14	14	7	SER	SER	PHE	PHE	D	D	15 - 1286	15 - 1286
15	15	8	SER	SER	PHE	PHE	B	B	15 - 1286	15 - 1286
16	16	8	SER	SER	PHE	PHE	E	E	15 - 1286	15 - 1286
17	17	9	SER	SER	THR	THR	B	B	15 - 1285	15 - 1285
18	18	9	SER	SER	THR	THR	F	F	15 - 1285	15 - 1285
19	19	10	SER	SER	PHE	PHE	C	C	7 - 1286	7 - 1286
20	20	10	SER	SER	PHE	PHE	D	D	7 - 1286	7 - 1286
21	21	11	SER	SER	THR	THR	C	C	15 - 1285	15 - 1285
22	22	11	SER	SER	THR	THR	E	E	15 - 1285	15 - 1285
23	23	12	SER	SER	THR	THR	C	C	7 - 1285	7 - 1285
24	24	12	SER	SER	THR	THR	F	F	7 - 1285	7 - 1285
25	25	13	SER	SER	PHE	PHE	D	D	15 - 1286	15 - 1286
26	26	13	SER	SER	PHE	PHE	E	E	15 - 1286	15 - 1286
27	27	14	ARG	ARG	PHE	PHE	D	D	6 - 1286	6 - 1286
28	28	14	ARG	ARG	PHE	PHE	F	F	6 - 1286	6 - 1286
29	29	15	SER	SER	THR	THR	E	E	15 - 1285	15 - 1285
30	30	15	SER	SER	THR	THR	F	F	15 - 1285	15 - 1285

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Beta-galactosidase / DUF4982 domain-containing protein Mass: 139785.828 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: 33-1336 construct from sequence corresponding to Uniprot entry A0A415C3Q2, starts after 32 amino-acid signal peptide, sequence conflict Glu/Asp (1165 in this entry, 1197 in Uniprot sequence) ...Details: 33-1336 construct from sequence corresponding to Uniprot entry A0A415C3Q2, starts after 32 amino-acid signal peptide, sequence conflict Glu/Asp (1165 in this entry, 1197 in Uniprot sequence) is due to a random mutation that occurred during cloning Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Gene: DW137_08020 / Production host: Bacillus licheniformis (bacteria) / References: UniProt: A0A415C3Q2, beta-galactosidase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H₂O
Compound details	The electron density for subunits E and F is poor and only interpretable at the level of secondary ...The electron density for subunits E and F is poor and only interpretable at the level of secondary structure elements, but not at the level of individual residues.
Has ligand of interest	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: 2.4 Å³/Da / Density % sol: 65.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 1.6 M ammonium sulfate, sodium acetate pH 4.6

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9795 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 30, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.89→199.58 Å / Num. obs: 252478 / % possible obs: 96.2 % / Redundancy: 3.6 % / B_iso Wilson estimate: 84.7 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.087 / R_rim(I) all: 0.123 / Net I/σ(I): 4.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
15.82-199.58	3.5	0.021	15.7	5108	0.999	0.021	0.03	0.22	90.6
2.89-2.94	3.7	1.514	0.5	12811	0.355	1.514	2.141	0.47	98.4

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Processing

Software

Name	Version	Classification
autoPROC		data scaling
Aimless		data reduction
MOLREP		phasing
REFMAC	5.8.0267	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5dmy, 1gof, 2w1s, 2wdc, 3f2z and 4lpl

Resolution: 2.89→199.578 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.928 / WR_factor R_free: 0.25 / WR_factor R_work: 0.221 / SU B: 23.17 / SU ML: 0.386 / Average fsc free: 0.7789 / Average fsc work: 0.79 / Cross valid method: FREE R-VALUE / ESU R: 1.191 / ESU R Free: 0.355 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.247	12540	4.976 %
R_work	0.2141	239474	-
all	0.216	-	-
obs	-	252014	96.234 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 113.059 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.589 Å²	-1.162 Å²	1.388 Å²
2-	-	1.185 Å²	-5.199 Å²
3-	-	-	2.947 Å²

Refinement step

Cycle: LAST / Resolution: 2.89→199.578 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	55787	0	74	6	55867

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	57061
X-RAY DIFFRACTION	r_angle_refined_deg	1.259	1.637	77802
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.912	5	7432
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.641	23.758	2650
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.354	15	8539
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.941	15	222
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	7886
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	43727
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	23657
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	38665
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.122	0.2	1756
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.274	0.2	74
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.099	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	11.412	11.441	29803
X-RAY DIFFRACTION	r_mcangle_it	16.808	17.145	37194
X-RAY DIFFRACTION	r_scbond_it	12.603	11.228	27258
X-RAY DIFFRACTION	r_scangle_it	17.854	16.812	40608
X-RAY DIFFRACTION	r_lrange_it	23.574	213.972	242531
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.063	0.05	39328
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.049	0.05	40161
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.049	0.05	40243
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.066	0.05	39177
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.046	0.05	40114
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.062	0.05	39309
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.062	0.05	39374
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.054	0.05	39490
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.062	0.05	39283
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.054	0.05	40206
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.069	0.05	39050
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.056	0.05	39997
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.067	0.05	39109
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.052	0.05	40047
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.06	0.05	39232

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.0635	0.05013
1	2	B	X-RAY DIFFRACTION	Local ncs	0.0635	0.05013
2	3	A	X-RAY DIFFRACTION	Local ncs	0.04879	0.05013
2	4	C	X-RAY DIFFRACTION	Local ncs	0.04879	0.05013
3	5	A	X-RAY DIFFRACTION	Local ncs	0.04905	0.05013
3	6	D	X-RAY DIFFRACTION	Local ncs	0.04905	0.05013
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06646	0.05013
4	8	E	X-RAY DIFFRACTION	Local ncs	0.06646	0.05013
5	9	A	X-RAY DIFFRACTION	Local ncs	0.04613	0.05013
5	10	F	X-RAY DIFFRACTION	Local ncs	0.04613	0.05013
6	11	B	X-RAY DIFFRACTION	Local ncs	0.06187	0.05013
6	12	C	X-RAY DIFFRACTION	Local ncs	0.06187	0.05013
7	13	B	X-RAY DIFFRACTION	Local ncs	0.06206	0.05013
7	14	D	X-RAY DIFFRACTION	Local ncs	0.06206	0.05013
8	15	B	X-RAY DIFFRACTION	Local ncs	0.05431	0.05013
8	16	E	X-RAY DIFFRACTION	Local ncs	0.05431	0.05013
9	17	B	X-RAY DIFFRACTION	Local ncs	0.06223	0.05013
9	18	F	X-RAY DIFFRACTION	Local ncs	0.06223	0.05013
10	19	C	X-RAY DIFFRACTION	Local ncs	0.05377	0.05013
10	20	D	X-RAY DIFFRACTION	Local ncs	0.05377	0.05013
11	21	C	X-RAY DIFFRACTION	Local ncs	0.06902	0.05013
11	22	E	X-RAY DIFFRACTION	Local ncs	0.06902	0.05013
12	23	C	X-RAY DIFFRACTION	Local ncs	0.05608	0.05013
12	24	F	X-RAY DIFFRACTION	Local ncs	0.05608	0.05013
13	25	D	X-RAY DIFFRACTION	Local ncs	0.06674	0.05013
13	26	E	X-RAY DIFFRACTION	Local ncs	0.06674	0.05013
14	27	D	X-RAY DIFFRACTION	Local ncs	0.05238	0.05013
14	28	F	X-RAY DIFFRACTION	Local ncs	0.05238	0.05013
15	29	E	X-RAY DIFFRACTION	Local ncs	0.06043	0.05013
15	30	F	X-RAY DIFFRACTION	Local ncs	0.06043	0.05013

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.89-2.965	0.395	933	0.388	18085	0.389	19330	0.486	0.496	98.3859	0.391
2.965-3.046	0.394	915	0.384	17641	0.385	18851	0.4	0.411	98.4351	0.386
3.046-3.135	0.36	898	0.347	17230	0.348	18406	0.482	0.483	98.4896	0.348
3.135-3.231	0.341	867	0.313	16724	0.314	17845	0.657	0.677	98.5766	0.309
3.231-3.337	0.303	859	0.28	16195	0.281	17317	0.755	0.768	98.4813	0.272
3.337-3.454	0.3	849	0.265	15587	0.267	16679	0.798	0.816	98.5431	0.257
3.454-3.584	0.29	835	0.249	15129	0.251	16163	0.842	0.862	98.7688	0.241
3.584-3.731	0.29	432	0.246	8827	0.248	15457	0.841	0.863	59.9017	0.24
3.731-3.897	0.24	721	0.207	13994	0.209	14915	0.909	0.922	98.6591	0.201
3.897-4.087	0.228	700	0.189	13313	0.191	14224	0.923	0.934	98.5166	0.184
4.087-4.308	0.207	663	0.17	12714	0.172	13540	0.939	0.949	98.7962	0.168
4.308-4.569	0.198	634	0.157	12007	0.159	12784	0.948	0.957	98.8814	0.157
4.569-4.884	0.184	566	0.15	11325	0.151	12035	0.957	0.962	98.8035	0.153
4.884-5.275	0.213	545	0.167	10482	0.17	11188	0.941	0.953	98.561	0.173
5.275-5.778	0.23	530	0.184	9623	0.186	10247	0.934	0.945	99.0827	0.191
5.778-6.459	0.253	427	0.196	8831	0.199	9363	0.923	0.941	98.8786	0.207
6.459-7.457	0.242	394	0.206	7640	0.208	8186	0.928	0.938	98.1432	0.223
7.457-9.13	0.205	387	0.186	6462	0.187	6961	0.947	0.95	98.391	0.208
9.13-12.899	0.217	253	0.191	4967	0.192	5358	0.943	0.951	97.4244	0.22
12.899-199.578	0.298	124	0.316	2609	0.315	2930	0.881	0.87	93.2765	0.548

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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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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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi