PDB-7cbs: Crystal structure of SpaB basal pilin from Lactobacillus rhamnosus GG

ID or keywords:

Entry

Database: PDB / ID: 7cbs

Title

Crystal structure of SpaB basal pilin from Lactobacillus rhamnosus GG

Components

LPXTG cell wall anchor domain-containing protein

Keywords

CELL ADHESION / Basal pilin / SpaCBA pilus / pilus anchoring / sortase / probiotics / isopeptide

Function / homology

Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / membrane => GO:0016020 / Immunoglobulin-like fold / LPXTG cell wall anchor domain-containing protein

Function and homology information

Biological species

Lactobacillus rhamnosus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.39 Å

Authors

Megta, A.K. / Pratap, S. / Kant, A. / Krishnan, V.

Funding support

India, 1items

Citation

Journal: Curr Res Struct Biol / Year: 2020
Title: Crystal structure of the atypically adhesive SpaB basal pilus subunit: Mechanistic insights about its incorporation in lactobacillar SpaCBA pili.
Authors: Megta, A.K. / Pratap, S. / Kant, A. / Palva, A. / von Ossowski, I. / Krishnan, V.

History

Deposition	Jun 13, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7cbs.cif.gz	386 KB	Display	PDBx/mmCIF format
PDB format	pdb7cbs.ent.gz	314.8 KB	Display	PDB format
PDBx/mmJSON format	7cbs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7cbs_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	7cbs_full_validation.pdf.gz	2.3 MB	Display
Data in XML	7cbs_validation.xml.gz	33.4 KB	Display
Data in CIF	7cbs_validation.cif.gz	45.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cb/7cbs ftp://data.pdbj.org/pub/pdb/validation_reports/cb/7cbs	HTTPS FTP

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Related structure data

Similar structure data	3rkq-d 5ev0-d 1q3b-d 3cwx-2 2jj6-d 6lnn-1 5mc7-d 5fce-d 6lz6-1 6a86-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) 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: LPXTG cell wall anchor domain-containing protein

B: LPXTG cell wall anchor domain-containing protein

C: LPXTG cell wall anchor domain-containing protein

D: LPXTG cell wall anchor domain-containing protein

E: LPXTG cell wall anchor domain-containing protein

G: LPXTG cell wall anchor domain-containing protein

F: LPXTG cell wall anchor domain-containing protein

L: LPXTG cell wall anchor domain-containing protein

hetero molecules

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

1

A: LPXTG cell wall anchor domain-containing protein

E: LPXTG cell wall anchor domain-containing protein

hetero molecules

defined by author&software
Evidence: gel filtration, monomeric
37.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: LPXTG cell wall anchor domain-containing protein

L: LPXTG cell wall anchor domain-containing protein

hetero molecules

defined by author&software
37.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: LPXTG cell wall anchor domain-containing protein

G: LPXTG cell wall anchor domain-containing protein

hetero molecules

defined by author&software
37.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: LPXTG cell wall anchor domain-containing protein

F: LPXTG cell wall anchor domain-containing protein

hetero molecules

defined by author&software
37.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.526, 51.526, 408.208
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-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	ALA	ALA	LYS	LYS	A	A	32 - 182	23 - 173
2	1	ALA	ALA	LYS	LYS	B	B	32 - 182	23 - 173
1	2	ALA	ALA	ASN	ASN	A	A	32 - 183	23 - 174
2	2	ALA	ALA	ASN	ASN	C	C	32 - 183	23 - 174
1	3	THR	THR	ASN	ASN	A	A	33 - 183	24 - 174
2	3	THR	THR	ASN	ASN	D	D	33 - 183	24 - 174
1	4	VAL	VAL	ASN	ASN	A	A	34 - 183	25 - 174
2	4	VAL	VAL	ASN	ASN	E	E	34 - 183	25 - 174
1	5	THR	THR	ASN	ASN	A	A	33 - 183	24 - 174
2	5	THR	THR	ASN	ASN	G	F	33 - 183	24 - 174
1	6	THR	THR	ASN	ASN	A	A	33 - 183	24 - 174
2	6	THR	THR	ASN	ASN	L	H	33 - 183	24 - 174
1	7	ALA	ALA	ASN	ASN	B	B	32 - 183	23 - 174
2	7	ALA	ALA	ASN	ASN	C	C	32 - 183	23 - 174
1	8	THR	THR	ASN	ASN	B	B	33 - 183	24 - 174
2	8	THR	THR	ASN	ASN	D	D	33 - 183	24 - 174
1	9	VAL	VAL	ASN	ASN	B	B	34 - 183	25 - 174
2	9	VAL	VAL	ASN	ASN	E	E	34 - 183	25 - 174
1	10	THR	THR	ASN	ASN	B	B	33 - 183	24 - 174
2	10	THR	THR	ASN	ASN	G	F	33 - 183	24 - 174
1	11	THR	THR	ASN	ASN	B	B	33 - 183	24 - 174
2	11	THR	THR	ASN	ASN	L	H	33 - 183	24 - 174
1	12	THR	THR	ASN	ASN	C	C	33 - 183	24 - 174
2	12	THR	THR	ASN	ASN	D	D	33 - 183	24 - 174
1	13	VAL	VAL	ASN	ASN	C	C	34 - 183	25 - 174
2	13	VAL	VAL	ASN	ASN	E	E	34 - 183	25 - 174
1	14	THR	THR	ASN	ASN	C	C	33 - 183	24 - 174
2	14	THR	THR	ASN	ASN	G	F	33 - 183	24 - 174
1	15	THR	THR	ASN	ASN	C	C	33 - 183	24 - 174
2	15	THR	THR	ASN	ASN	L	H	33 - 183	24 - 174
1	16	VAL	VAL	ASN	ASN	D	D	34 - 183	25 - 174
2	16	VAL	VAL	ASN	ASN	E	E	34 - 183	25 - 174
1	17	THR	THR	ASN	ASN	D	D	33 - 183	24 - 174
2	17	THR	THR	ASN	ASN	G	F	33 - 183	24 - 174
1	18	THR	THR	ASN	ASN	D	D	33 - 183	24 - 174
2	18	THR	THR	ASN	ASN	L	H	33 - 183	24 - 174
1	19	VAL	VAL	ASN	ASN	E	E	34 - 183	25 - 174
2	19	VAL	VAL	ASN	ASN	G	F	34 - 183	25 - 174
1	20	VAL	VAL	ASN	ASN	E	E	34 - 183	25 - 174
2	20	VAL	VAL	ASN	ASN	L	H	34 - 183	25 - 174
1	21	THR	THR	ASN	ASN	G	F	33 - 183	24 - 174
2	21	THR	THR	ASN	ASN	L	H	33 - 183	24 - 174

NCS ensembles :

#1: Protein	LPXTG cell wall anchor domain-containing protein Mass: 18880.018 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Gene: F8M46_02260 / Variant: ATCC 53103/GG / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A5P5Z9C8
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.17 Å³/Da / Density % sol: 43.42 % / Description: Three-dimensional hexagonal shaped crystals
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Magnesium chloride, 0.1 M MES pH 6.5, and 30% (w/v) PEG 4000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: BM14 / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.259
1	1	K, H, -L	2	0.25
1	1	-K, -H, -L	3	0.246
1	1	-h,-k,l	4	0.245

Reflection

Resolution: 2.39→43.59 Å / Num. obs: 41158 / % possible obs: 93.2 % / Redundancy: 3.7 % / B_iso Wilson estimate: 55.2 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.045 / R_pim(I) all: 0.026 / R_rim(I) all: 0.052 / Net I/σ(I): 15

Reflection shell

Resolution: 2.39→2.47 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / Num. unique obs: 2058 / CC_1/2: 0.71 / R_pim(I) all: 0.29 / R_rim(I) all: 0.52 / % possible all: 72.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.39→43.59 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.903 / SU B: 9.103 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22789	2145	5.2 %	RANDOM
R_work	0.19036	-	-	-
obs	0.19228	39014	86.2 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 69.271 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	17.85 Å²	0 Å²	0 Å²
2-	-	17.85 Å²	0 Å²
3-	-	-	-35.71 Å²

Refinement step

Cycle: 1 / Resolution: 2.39→43.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7188	0	7	75	7270

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.013	7427
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	6529
X-RAY DIFFRACTION	r_angle_refined_deg	1.276	1.632	10134
X-RAY DIFFRACTION	r_angle_other_deg	1.101	1.569	15100
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.241	5	983
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.184	25.446	303
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.961	15	1011
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.271	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.034	0.2	1035
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	8444
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1390
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	1.442	2.823	3992
X-RAY DIFFRACTION	r_mcbond_other	1.442	2.823	3991
X-RAY DIFFRACTION	r_mcangle_it	2.359	4.234	4955
X-RAY DIFFRACTION	r_mcangle_other	2.359	4.234	4956
X-RAY DIFFRACTION	r_scbond_it	1.192	2.764	3435
X-RAY DIFFRACTION	r_scbond_other	1.136	2.763	3424
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.698	4.143	5179
X-RAY DIFFRACTION	r_long_range_B_refined	4.023	32.135	7180
X-RAY DIFFRACTION	r_long_range_B_other	4.021	32.137	7179
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	3564	0.08
1	2	B	3564	0.08
2	1	A	3568	0.07
2	2	C	3568	0.07
3	1	A	3553	0.08
3	2	D	3553	0.08
4	1	A	3338	0.09
4	2	E	3338	0.09
5	1	A	3433	0.08
5	2	G	3433	0.08
6	1	A	3425	0.08
6	2	L	3425	0.08
7	1	B	3596	0.07
7	2	C	3596	0.07
8	1	B	3571	0.07
8	2	D	3571	0.07
9	1	B	3350	0.09
9	2	E	3350	0.09
10	1	B	3464	0.08
10	2	G	3464	0.08
11	1	B	3424	0.09
11	2	L	3424	0.09
12	1	C	3517	0.07
12	2	D	3517	0.07
13	1	C	3320	0.09
13	2	E	3320	0.09
14	1	C	3432	0.06
14	2	G	3432	0.06
15	1	C	3380	0.09
15	2	L	3380	0.09
16	1	D	3293	0.09
16	2	E	3293	0.09
17	1	D	3438	0.06
17	2	G	3438	0.06
18	1	D	3390	0.09
18	2	L	3390	0.09
19	1	E	3313	0.08
19	2	G	3313	0.08
20	1	E	3244	0.1
20	2	L	3244	0.1
21	1	G	3357	0.08
21	2	L	3357	0.08

LS refinement shell

Resolution: 2.395→2.457 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.237	81	-
R_work	0.194	1527	-
obs	-	-	44.75 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.9352	2.2896	2.2155	3.2875	1.894	5.836	0.045	-0.3092	-0.226	0.3084	-0.0807	-0.22	-0.4737	-0.0839	0.0356	0.1437	-0.0563	-0.1408	0.3933	0.0248	0.5985	12.992	1.622	-10.784
2	1.7881	-0.1289	-0.3876	6.4437	2.6018	5.1946	-0.0346	-0.247	0.1002	0.3529	0.042	-0.1543	-0.1344	-0.3508	-0.0075	0.3615	-0.0934	-0.0852	0.139	-0.0703	0.5187	30.726	-3.079	-78.77
3	1.8955	0.0556	0.2002	6.5192	2.1787	4.5509	0.0004	0.1999	-0.1099	-0.3586	-0.027	-0.098	0.0826	-0.3261	0.0266	0.3076	0.0845	0.0844	0.1004	-0.0662	0.4784	4.919	-11.919	-57.703
4	6.2572	2.3852	2.4582	3.0378	1.3018	5.1737	-0.0721	0.3194	-0.1961	-0.1667	0.0722	-0.0037	-0.3411	-0.3608	-0	0.2472	-0.1311	-0.0507	0.222	-0.1019	0.5417	17.462	-24.932	10.463
5	7.825	0.5924	0.2746	5.95	0.0677	5.1517	-0.2389	1.0301	-0.073	-1.0576	0.2579	0.5346	-0.0423	-0.2743	-0.0191	0.2136	-0.1332	-0.1514	0.5859	-0.0501	0.478	35.752	-4.954	-30.699
6	7.0269	2.7056	-0.7082	8.3205	-0.1434	4.0206	0.1339	-0.9198	0.243	0.5437	-0.0649	-0.4287	-0.1333	0.1668	-0.0689	0.2672	-0.1962	-0.0941	0.3144	-0.0649	0.4371	12.731	-49.452	27.381
7	6.0445	-0.7427	-0.4657	8.0416	1.2036	4.3975	0.1515	-0.7626	0.3768	1.2084	-0.1391	0.2239	-0.1398	-0.1444	-0.0124	0.5537	0.0884	0.05	0.1667	-0.1066	0.4676	22.285	-28.664	-38.307
8	5.2103	0.3136	0.3277	8.245	0.7562	4.5785	0.1244	0.7435	-0.4616	-1.2859	-0.1417	0.1764	0.1918	-0.1209	0.0173	0.5674	-0.083	-0.0368	0.1633	-0.1229	0.4821	48.244	13.587	-97.951

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	31 - 183
2	X-RAY DIFFRACTION	2	B	32 - 183
3	X-RAY DIFFRACTION	3	C	32 - 183
4	X-RAY DIFFRACTION	4	D	33 - 183
5	X-RAY DIFFRACTION	5	E	34 - 183
6	X-RAY DIFFRACTION	6	F	33 - 181
7	X-RAY DIFFRACTION	7	G	33 - 183
8	X-RAY DIFFRACTION	8	L	33 - 183

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