PDB-5hts: Crystal structure of shaft pilin spaA from Lactobacillus rhamnosu...

ID or keywords:

Entry

Database: PDB / ID: 5hts

Title

Crystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG - D295N mutant

Components

Cell surface protein SpaA

Keywords

CELL ADHESION / Pilin / spaA / probiotic / isopeptide / SpaCBA pili / adhesin

Function / homology

Function and homology information

Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...
Similarity search - Domain/homology

Biological species

Lactobacillus rhamnosus GG (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Chaurasia, P. / Pratap, S. / von Ossowski, I. / Palva, A. / Krishnan, V.

Funding support

India, 1items

Citation

Journal: Sci Rep / Year: 2016
Title: New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit
Authors: Chaurasia, P. / Pratap, S. / von Ossowski, I. / Palva, A. / Krishnan, V.

History

Deposition	Jan 27, 2016	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 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_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5hts.cif.gz	591.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5hts.ent.gz	494.5 KB	Display	PDB format
PDBx/mmJSON format	5hts.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5hts_validation.pdf.gz	473.3 KB	Display	wwPDB validaton report
Full document	5hts_full_validation.pdf.gz	478.3 KB	Display
Data in XML	5hts_validation.xml.gz	51.7 KB	Display
Data in CIF	5hts_validation.cif.gz	72.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ht/5hts ftp://data.pdbj.org/pub/pdb/validation_reports/ht/5hts	HTTPS FTP

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Related structure data

Related structure data	5f44SC 5faaC 5fgrC 5fgsC 5fieC 5hbbC 5hdlC 5j4mC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5f44-1 5f44-2 5j4m-3 5j4m-2 5f44-3 5hdl-3 5hdl-1 5hdl-2 5j4m-1 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 - HomologyF&H Search

Related structure data

5f44SC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cell surface protein SpaA

B: Cell surface protein SpaA

C: Cell surface protein SpaA

D: Cell surface protein SpaA

E: Cell surface protein SpaA

F: Cell surface protein SpaA

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

1

A: Cell surface protein SpaA

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

2

B: Cell surface protein SpaA

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

3

C: Cell surface protein SpaA

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

4

D: Cell surface protein SpaA

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

5

E: Cell surface protein SpaA

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

6

F: Cell surface protein SpaA

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

Unit cell

Length a, b, c (Å)	164.328, 75.161, 176.476
Angle α, β, γ (deg.)	90.00, 100.30, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	39 - 302
2	1	B	39 - 302
1	2	A	39 - 302
2	2	C	39 - 302
1	3	A	39 - 301
2	3	D	39 - 301
1	4	A	39 - 301
2	4	E	39 - 301
1	5	A	62 - 301
2	5	F	42 - 301
1	6	B	39 - 302
2	6	C	39 - 302
1	7	B	39 - 302
2	7	D	39 - 302
1	8	B	39 - 301
2	8	E	39 - 301
1	9	B	62 - 301
2	9	F	42 - 301
1	10	C	39 - 302
2	10	D	39 - 302
1	11	C	39 - 302
2	11	E	39 - 302
1	12	C	40 - 301
2	12	F	40 - 301
1	13	D	39 - 301
2	13	E	39 - 301
1	14	D	62 - 301
2	14	F	42 - 301
1	15	E	40 - 302
2	15	F	40 - 302

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Cell surface protein SpaA Mass: 30722.514 Da / Num. of mol.: 6 / Fragment: UNP residues 35-302 / Mutation: D295N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus rhamnosus GG (bacteria) / Strain: GG / Gene: LRHM_0426 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: C7T9P4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.02 Å³/Da / Density % sol: 59.25 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, 15%(w/v) PEG 20000 / PH range: 8.0 - 8.7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95371 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95371 Å / Relative weight: 1
Reflection	Resolution: 2.6→37.9 Å / Num. obs: 64379 / % possible obs: 98.6 % / Redundancy: 4.3 % / R_merge(I) obs: 0.054 / Net I/σ(I): 14.4
Reflection shell	Resolution: 2.6→2.74 Å / Redundancy: 4 % / R_merge(I) obs: 0.274 / Mean I/σ(I) obs: 3.6 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
XDS		data processing
Aimless		data scaling
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5F44

5f44

Resolution: 2.6→37.9 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.919 / SU B: 26.595 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.606 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2653	3262	5.1 %	RANDOM
R_work	0.24197	-	-	-
obs	0.24316	61114	98.64 %	-

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: 64.46 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.68 Å²	0 Å²	-0.54 Å²
2-	-	0.11 Å²	0 Å²
3-	-	-	0.72 Å²

Refinement step

Cycle: 1 / Resolution: 2.6→37.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11576	0	0	236	11812

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.02	11938
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	10800
X-RAY DIFFRACTION	r_angle_refined_deg	1.48	1.938	16241
X-RAY DIFFRACTION	r_angle_other_deg	1.11	3	24960
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.997	5	1538
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.942	25.595	529
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.994	15	1831
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.698	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	1830
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	13811
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	2681
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	1.678	2.214	6125
X-RAY DIFFRACTION	r_mcbond_other	1.678	2.214	6124
X-RAY DIFFRACTION	r_mcangle_it	2.706	3.314	7642
X-RAY DIFFRACTION	r_mcangle_other	2.706	3.314	7643
X-RAY DIFFRACTION	r_scbond_it	1.768	2.348	5813
X-RAY DIFFRACTION	r_scbond_other	1.768	2.348	5814
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.775	3.453	8590
X-RAY DIFFRACTION	r_long_range_B_refined	6.212	17.99	13192
X-RAY DIFFRACTION	r_long_range_B_other	6.203	17.95	13173
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	14445	0.04
1	2	B	14445	0.04
2	1	A	14321	0.04
2	2	C	14321	0.04
3	1	A	14331	0.05
3	2	D	14331	0.05
4	1	A	13645	0.04
4	2	E	13645	0.04
5	1	A	12688	0.05
5	2	F	12688	0.05
6	1	B	14310	0.04
6	2	C	14310	0.04
7	1	B	14325	0.06
7	2	D	14325	0.06
8	1	B	13629	0.04
8	2	E	13629	0.04
9	1	B	12707	0.05
9	2	F	12707	0.05
10	1	C	14413	0.04
10	2	D	14413	0.04
11	1	C	13702	0.04
11	2	E	13702	0.04
12	1	C	13561	0.04
12	2	F	13561	0.04
13	1	D	13616	0.04
13	2	E	13616	0.04
14	1	D	12663	0.06
14	2	F	12663	0.06
15	1	E	13565	0.04
15	2	F	13565	0.04

LS refinement shell

Resolution: 2.604→2.672 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.366	232	-
R_work	0.327	4349	-
obs	-	-	95.26 %

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	1.6642	-0.1866	0.8323	1.9518	-0.834	4.6481	0.0852	0.5653	0.1806	-0.2695	-0.3139	-0.0822	0.0332	0.2375	0.2288	0.4726	0.2089	-0.3196	0.4278	0.0061	0.3017	-30.124	3.502	49.025
2	3.8981	-1.258	2.2255	1.9171	-1.5904	3.3978	0.2465	0.2805	-0.1133	-0.1199	-0.1161	0.1783	0.0665	0.0721	-0.1304	0.3437	0.1838	-0.2329	0.1727	-0.0515	0.2415	-5.314	-18.073	70.69
3	1.9855	0.1799	0.8927	1.5683	-0.867	4.5665	0.0884	0.4812	0.063	-0.2561	-0.1703	0.0565	-0.2787	0.0388	0.0819	0.5123	0.2375	-0.3246	0.4139	0.0074	0.3084	-29.277	40.769	51.049
4	2.9789	-1.1316	2.5713	1.9671	-2.3391	4.5252	0.2786	0.2081	-0.1062	-0.0455	-0.1073	0.1396	0.0646	0.0095	-0.1713	0.2522	0.1138	-0.2307	0.0876	-0.0898	0.2484	-4.311	19.36	72.772
5	3.8625	0.1867	1.0544	0.2981	0.681	3.1304	0.2395	-0.0116	-0.3211	-0.0011	-0.1761	-0.042	0.3646	-0.2322	-0.0635	0.3785	0.0586	-0.2936	0.1208	0.0068	0.3301	-49.08	4.159	71.846
6	3.2294	0.4417	1.8992	2.1271	0.5938	4.7793	-0.0328	0.4944	-0.331	-0.4573	0.0885	-0.0027	0.0053	-0.4573	-0.0557	0.4137	0.0297	-0.2603	0.4533	-0.1531	0.2563	-75.357	1.06	42.579
7	2.1063	-0.2316	1.2432	0.1911	0.3434	3.6663	0.2856	0.1379	-0.0603	-0.07	-0.1259	-0.0158	0.1635	-0.0601	-0.1597	0.3071	0.0747	-0.2771	0.1054	-0.0176	0.298	-48.082	41.786	73.962
8	3.0293	0.9797	2.7276	1.8481	1.0482	5.4496	0.0515	0.3759	-0.2697	-0.2928	0.0359	-0.0405	0.0139	-0.3135	-0.0875	0.3643	0.1019	-0.2611	0.377	-0.1063	0.2403	-74.296	38.789	44.564
9	2.2745	-0.6805	2.1942	1.4108	-0.1688	5.3547	-0.0085	0.0302	-0.2055	0.2383	0.199	-0.0596	0.1939	0.2259	-0.1905	0.6346	0.1082	-0.3804	0.7794	0.2274	0.3661	-66.053	27.897	-15.437
10	1.6737	-0.6072	2.9393	2.301	-2.0733	6.7437	0.0672	0.0373	-0.0861	-0.0803	0.0374	0.1899	0.1752	-0.1589	-0.1046	0.625	0.2019	-0.3154	0.6281	0.1296	0.3105	-52.322	15.247	19.225
11	2.9133	0.5127	2.2391	2.3945	-1.1037	4.4981	0.061	-0.1134	0.0712	-0.2958	0.2158	0.4946	0.3279	0.0376	-0.2768	0.8523	-0.2514	-0.4919	0.8936	-0.3206	0.6426	-15.61	25.407	14.576
12	0.8783	0.0577	1.9238	1.4426	0.5991	5.7617	-0.1248	0.0631	0.083	0.0628	0.008	-0.3946	-0.3535	0.4832	0.1168	0.9149	-0.3256	-0.5131	0.8008	-0.1553	0.5582	-30.663	14.969	-21.064

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	39 - 176
2	X-RAY DIFFRACTION	2	A	177 - 302
3	X-RAY DIFFRACTION	3	B	39 - 176
4	X-RAY DIFFRACTION	4	B	177 - 302
5	X-RAY DIFFRACTION	5	C	39 - 176
6	X-RAY DIFFRACTION	6	C	177 - 299
7	X-RAY DIFFRACTION	7	D	38 - 176
8	X-RAY DIFFRACTION	8	D	177 - 302
9	X-RAY DIFFRACTION	9	E	39 - 176
10	X-RAY DIFFRACTION	10	E	177 - 301
11	X-RAY DIFFRACTION	11	F	40 - 176
12	X-RAY DIFFRACTION	12	F	177 - 302

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