PDB-5y9g: Crystal structure of Salmonella SafD adhesin

ID or keywords:

Entry

Database: PDB / ID: 5y9g

Title

Crystal structure of Salmonella SafD adhesin

Components

Pilin structural protein SafD,Pilus assembly protein

Keywords

CELL ADHESION / host recognition / biofilm formation / Salmonella atypical fimbriae / poly-adhesive activity / self-associating oligomerization

Function / homology

: / :

Function and homology information

Biological species

Salmonella enteritidis (bacteria)

Salmonella choleraesuis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Zeng, L.H. / Zhang, L. / Wang, P.R. / Meng, G.

Funding support

China, 2items

Citation

Journal: Elife / Year: 2017
Title: Structural basis of host recognition and biofilm formation by Salmonella Saf pili
Authors: Zeng, L.H. / Zhang, L. / Wang, P.R. / Meng, G.

History

Deposition	Aug 25, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5y9g.cif.gz	165.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5y9g_validation.pdf.gz	432.3 KB	Display	wwPDB validaton report
Full document	5y9g_full_validation.pdf.gz	433.8 KB	Display
Data in XML	5y9g_validation.xml.gz	13.1 KB	Display
Data in CIF	5y9g_validation.cif.gz	17.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y9/5y9g ftp://data.pdbj.org/pub/pdb/validation_reports/y9/5y9g	HTTPS FTP

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Related structure data

Related structure data	5y9hC 2ixqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3zpv-1 3zpv-11 4or1-1 3di5-d 4lw9-11 3zpv-18 6c4u-6 6c4u-5 4ysi-d 3zpv-13 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Pilin structural protein SafD,Pilus assembly protein

B: Pilin structural protein SafD,Pilus assembly protein

32.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pilin structural protein SafD,Pilus assembly protein

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

2

B: Pilin structural protein SafD,Pilus assembly protein

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

Unit cell

Length a, b, c (Å)	32.300, 49.710, 148.830
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Pilin structural protein SafD,Pilus assembly protein Mass: 16284.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enteritidis (bacteria), (gene. exp.) Salmonella choleraesuis (bacteria) Gene: R567_09630, IN36_14140 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1X2WLP6, UniProt: A0A158MX89
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	Authors state that the sequence DNKQ is an artificial linker.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.83 Å³/Da / Density % sol: 32.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 10, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.2→74.4 Å / Num. obs: 11971 / % possible obs: 98 % / Redundancy: 4 % / R_merge(I) obs: 0.195 / Net I/σ(I): 6.8
Reflection shell	Resolution: 2.2→2.32 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.679 / CC_1/2: 0.52 / % possible all: 88.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2IXQ

2ixq

Resolution: 2.2→47.15 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.52

	R_factor	Num. reflection	% reflection
R_free	0.2326	588	5.07 %
R_work	0.1989	-	-
obs	0.2006	11606	90.36 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.2→47.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2130	0	0	125	2255

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2178
X-RAY DIFFRACTION	f_angle_d	0.666	2963
X-RAY DIFFRACTION	f_dihedral_angle_d	14.664	1263
X-RAY DIFFRACTION	f_chiral_restr	0.048	325
X-RAY DIFFRACTION	f_plane_restr	0.004	391

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2001-2.4215	0.3306	133	0.2569	2624	X-RAY DIFFRACTION	88
2.4215-2.7718	0.2768	143	0.2306	2604	X-RAY DIFFRACTION	87
2.7718-3.492	0.2207	140	0.1965	2732	X-RAY DIFFRACTION	90
3.492-10	0.1956	172	0.1685	3058	X-RAY DIFFRACTION	96

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	2.429	-2.225	-0.5636	3.9307	1.052	8.6487	0.1364	0.5394	-0.4865	0.0226	0.014	1.1926	1.1372	-1.6829	0.1134	-0.0176	0.2145	0.0021	0.1258	0.0193	0.5112	20.2115	21.0847	14.4812
2	5.2071	-1.5792	-0.7628	5.9625	0.9383	6.1975	-0.0275	-0.6875	-0.2543	0.5202	-0.1199	0.0093	0.3098	-0.1933	0.0438	0.2794	-0.09	-0.0367	0.2138	0.0033	0.1796	35.4194	41.4958	19.3521
3	2.0701	-0.0434	0.5703	1.1133	0.3908	3.3826	0.1475	-0.3094	-0.3596	-0.0811	-0.1294	-0.3686	0.3217	0.0675	0.0067	0.2236	0.0163	0.0271	0.0857	0.0547	0.0535	28.8618	26.3285	14.9865
4	3.0738	1.4734	-0.5671	5.2925	-0.5592	1.3667	0.1157	0.7074	0.2183	-0.4685	0.123	0.1017	0.1746	-0.1803	0.0737	0.4387	0.0111	-0.1299	0.1569	-0.0826	0.1259	24.9754	26.0058	2.8367
5	3.7444	-2.4413	-1.2204	6.6797	1.5695	2.0723	-0.3893	-0.2496	0.4284	0.3087	0.2025	0.1938	-0.3728	0.1084	0.1238	0.2619	-0.0234	-0.0782	0.1616	0.012	0.2302	26.8166	42.925	9.2636
6	5.6816	2.0911	3.5028	7.2178	-0.3369	2.9233	-0.0054	0.5852	0.0705	-0.8833	-0.2049	-0.2621	0.0584	0.505	0.0357	0.3142	0.0632	0.0182	0.2517	0.0105	0.1555	31.0037	25.8331	-0.2165
7	4.7092	-0.204	0.0726	5.0517	-1.0272	1.3927	0.2518	0.8808	-0.7474	-1.3377	-0.3299	-0.1362	1.0778	0.342	0.1604	0.441	0.0924	-0.0271	0.148	0.0544	0.2216	29.7408	16.6975	4.2634
8	2.5956	0.3441	1.2447	3.6497	0.4305	1.9866	-0.1729	-0.0188	0.3492	-0.1285	0.058	0.3456	-0.0977	0.0422	0.117	0.1506	0.0092	0.0144	0.1491	0.0239	0.1521	28.2535	35.498	11.4667
9	2.8989	-1.5654	-1.795	3.4335	0.464	3.6934	0.3074	0.4741	0.1028	0.1265	-0.7051	1.3794	-0.0727	-1.0767	-0.0151	0.3234	0.1011	0.0082	0.5234	0.0399	0.3861	20.5672	32.0531	13.7203
10	2.8803	0.9934	0.2122	3.5662	0.2782	2.2848	-0.0989	-0.2096	0.249	-0.143	-0.0711	0.2283	-0.2119	0.0455	0.1243	0.0963	0.0064	0.0173	0.1338	0.016	0.0893	36.0231	26.9213	24.4617
11	2.4704	0.3132	-2.7636	1.8953	-1.1778	3.5786	-0.064	-0.8264	-0.3861	-0.0058	0.3779	0.0202	0.4998	0.765	0.0451	0.1358	0.0429	0.0083	0.2252	0.0448	0.225	46.0022	15.9331	29.268
12	3.8502	3.0793	-4.4702	5.5599	-3.1003	7.4676	-0.5827	0.2979	-0.6925	-0.1881	0.0932	-0.6014	0.5342	-0.4719	0.2301	0.1381	0.0681	0.0154	0.2197	0.009	0.146	36.2558	11.1887	28.4666
13	3.2004	1.2708	0.5467	3.7651	1.0221	1.7509	0.0366	-0.097	0.2176	-0.2191	0.0035	-0.158	-0.2487	0.0521	-0.0061	0.1199	0.0051	0.0349	0.1494	0.0363	0.1301	46.0873	28.0502	22.867
14	1.5251	1.2952	-0.5988	5.5106	1.054	2.0306	-0.0198	-0.1698	0.1246	0.239	0.0922	-0.1209	-0.0722	0.2966	0.023	0.1443	0.0461	-0.0452	0.175	-0.0077	0.1243	36.9612	22.3936	29.7671

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 30 through 39 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 52 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 53 through 60 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 61 through 82 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 83 through 101 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 102 through 114 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 115 through 122 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 123 through 149 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 150 through 178 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 31 through 71 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 72 through 82 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 83 through 101 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 102 through 130 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 131 through 178 )

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