PDB-4tt9: Structure of the C-terminal SpoA domain of Shigella flexneri Spa33

ID or keywords:

Entry

Database: PDB / ID: 4tt9

Title

Structure of the C-terminal SpoA domain of Shigella flexneri Spa33

Components

Surface presentation of antigens protein SpaO

Keywords

PROTEIN TRANSPORT / T3SS / C-ring / SpoA / FliN / immune system

Function / homology

Function and homology information

protein secretion
Similarity search - Function

Biological species

Shigella flexneri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

McDowell, M.A. / Johnson, S. / Lea, S.M.

Citation

Journal: Mol.Microbiol. / Year: 2016
Title: Characterisation of Shigella Spa33 and Thermotoga FliM/N reveals a new model for C-ring assembly in T3SS.
Authors: McDowell, M.A. / Marcoux, J. / McVicker, G. / Johnson, S. / Fong, Y.H. / Stevens, R. / Bowman, L.A. / Degiacomi, M.T. / Yan, J. / Wise, A. / Friede, M.E. / Benesch, J.L. / Deane, J.E. / ...

History

Deposition	Jun 20, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 24, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 18, 2015	Group: Database references
Revision 1.2	Feb 24, 2016	Group: Database references
Revision 1.3	Dec 20, 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	4tt9.cif.gz	131.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4tt9.ent.gz	104.1 KB	Display	PDB format
PDBx/mmJSON format	4tt9.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tt/4tt9 ftp://data.pdbj.org/pub/pdb/validation_reports/tt/4tt9	HTTPS FTP

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Related structure data

Related structure data	1o9yS 1yabS S: Starting model for refinement
Similar structure data	4dhk-2 2g2q-3 1klp-d 1em9-1 1x5o-d 1b2p-d 1irl-d 4rd7-d 1jkq-d 4jue-4 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

Deposited unit

A: Surface presentation of antigens protein SpaO

B: Surface presentation of antigens protein SpaO

C: Surface presentation of antigens protein SpaO

D: Surface presentation of antigens protein SpaO

hetero molecules

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

1

A: Surface presentation of antigens protein SpaO

B: Surface presentation of antigens protein SpaO

hetero molecules

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

2

C: Surface presentation of antigens protein SpaO

D: Surface presentation of antigens protein SpaO

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.300, 27.820, 104.440
Angle α, β, γ (deg.)	90.00, 90.03, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Surface presentation of antigens protein SpaO / Spa33 protein Mass: 9884.185 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: C-terminal SpoA domain / Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: spaO, spa33, CP0152 / Plasmid: pET28b / Production host: Escherichia coli B (bacteria) / Strain (production host): B834(DE3) / Variant (production host): pLysS / References: UniProt: P0A1K9
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.89 Å³/Da / Density % sol: 35 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% (v/v) isopropanol, 0.1 M Na HEPES pH7.0, 10% (w/v) PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.3→51.3 Å / Num. obs: 13523 / % possible obs: 99.5 % / Redundancy: 3.6 % / R_merge(I) obs: 0.042 / Net I/σ(I): 21.3
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.77 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
XSCALE		data scaling
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1YAB, 1O9Y

1yab

1o9y

Resolution: 2.3→51.3 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.52 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2099	1369	10.12 %	Phenix selected for twin refinement
R_work	0.1739	-	-	-
obs	0.1768	13522	99.42 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→51.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2273	0	16	65	2354

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2323
X-RAY DIFFRACTION	f_angle_d	1.03	3124
X-RAY DIFFRACTION	f_dihedral_angle_d	15.14	854
X-RAY DIFFRACTION	f_chiral_restr	0.071	357
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 (%)
2.3026-2.3849	0.3645	127	0.324	1174	X-RAY DIFFRACTION	90
2.3849-2.4804	0.3597	140	0.3128	1208	X-RAY DIFFRACTION	89
2.4804-2.5933	0.3362	136	0.2916	1195	X-RAY DIFFRACTION	90
2.5933-2.73	0.3033	123	0.2587	1209	X-RAY DIFFRACTION	90
2.73-2.901	0.2462	134	0.237	1200	X-RAY DIFFRACTION	90
2.901-3.125	0.2767	128	0.2164	1237	X-RAY DIFFRACTION	90
3.125-3.4394	0.2218	132	0.1882	1222	X-RAY DIFFRACTION	90
3.4394-3.937	0.1754	147	0.1586	1215	X-RAY DIFFRACTION	89
3.937-4.9595	0.1714	137	0.1156	1206	X-RAY DIFFRACTION	89
4.9595-51.3127	0.1716	161	0.1347	1272	X-RAY DIFFRACTION	87

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	1.1758	1.7185	0.7563	2.8753	1.5752	1.1638	-0.4318	-0.7934	-0.8849	0.139	-0.4956	-0.4081	0.6648	0.2569	0.5052	0.4681	0.1541	0.1932	1.3048	0.4457	0.8499	38.0475	-13.3752	48.8198
2	7.3134	1.8974	1.5735	2.485	-1.1636	6.766	-0.5177	-0.3178	0.9485	0.1573	0.1905	0.2993	-0.4559	-0.2163	0.6591	0.3763	-0.0078	-0.0149	0.406	-0.1409	0.3747	15.2789	5.3828	42.6081
3	3.2815	1.0177	-2.6596	2.8184	-0.1909	3.0485	-0.5309	0.1572	1.8254	-0.6885	0.6044	0.0458	-0.0293	0.01	0.1184	0.4821	-0.045	-0.1324	0.4972	-0.0933	0.6237	19.1745	7.8157	33.1222
4	5.3184	-1.2088	1.6841	4.7844	1.3646	6.4202	-0.255	-0.2172	0.0425	-0.2938	-0.4011	-0.2029	-0.1674	-0.6296	0.7502	0.3719	-0.0232	0.1862	0.5359	-0.049	0.5267	31.0113	-1.2206	33.4577
5	6.1031	1.1313	6.938	6.6986	1.0271	7.8917	-0.0591	-0.616	-1.0302	-0.0285	-0.1617	-1.3008	-0.3268	2.567	-0.5958	0.393	-0.0881	0.0148	1.0522	0.0127	0.5576	39.7434	1.477	36.8528
6	2.7309	-1.667	2.7167	3.89	-0.1856	3.6588	0.0241	0.4559	0.06	0.0521	-0.5107	-0.0162	0.0737	-0.0744	0.5248	0.2993	-0.1135	0.0799	0.3716	0.061	0.3098	26.0589	-3.1077	44.4822
7	4.2664	0.9585	-1.0313	3.8046	0.9951	5.3071	-0.2453	-0.1132	-0.0286	-0.1542	-0.1393	0.1293	0.2996	0.2476	0.3653	0.3245	0.0051	0.0017	0.36	0.0331	0.3092	19.9172	-2.483	34.9331
8	3.1322	-0.3502	-2.479	0.7966	-0.8267	3.4735	-0.3325	-0.1685	-0.725	-0.1605	-0.2566	0.0396	0.5485	-0.0158	0.4391	0.4354	0.0139	0.083	0.3714	-0.0936	0.3729	-3.2212	-0.4223	7.5971
9	9.3607	0.0894	0.4537	4.0898	0.93	2.351	-0.1806	0.189	-0.6418	0.2431	0.1518	-0.3378	0.5501	0.0756	0.1014	0.3859	0.0077	0.0344	0.2905	0.0401	0.3521	0.0654	-2.7926	18.4656
10	9.5365	-3.671	-6.3364	6.7453	3.9601	7.5464	0.0797	0.6801	-1.1291	0.1926	-0.1936	-1.182	0.0141	0.4352	0.0293	0.4249	0.1221	-0.1247	0.7925	-0.0351	0.8809	11.9954	-0.6743	17.0646
11	4.4849	-0.3659	0.9881	0.6433	2.0631	6.9973	-0.4486	0.126	0.2188	0.0064	-0.2632	0.3263	0.3467	-0.3445	0.8461	0.3709	0.0118	0.0517	0.3749	0.0829	0.3968	-2.5041	0.8435	7.5185
12	2.8648	1.6102	-3.9061	3.8301	0.9231	8.7609	-0.3365	-1.2407	-0.9276	0.3817	0.0934	-0.2004	0.7265	0.0127	-0.5647	0.5803	-0.0865	-0.0109	1.0134	0.4241	0.5853	15.9854	7.0296	14.837
13	3.0761	-1.4072	3.9737	4.4755	-1.8229	5.1323	-0.1699	1.0671	0.7815	-1.126	-0.3694	0.0315	-0.9621	0.5156	0.5955	0.5593	0.1813	-0.1449	1.0572	0.2004	0.4909	7.9641	6.6765	23.2685
14	3.6322	4.3287	-4.9039	5.1737	-5.8453	6.6233	-0.6202	-1.4371	1.5846	0.3965	-0.2979	0.209	-0.9115	-0.2028	0.2589	0.752	0.3007	-0.3735	0.9672	-0.3472	0.5819	-3.7942	7.9973	23.7708
15	8.5344	-2.0958	-0.6305	6.0022	4.1048	7.388	0.0238	0.5948	0.1533	-0.5631	-0.4159	0.6575	-1.1119	-0.5385	0.2733	0.3422	0.0906	0.0435	0.4047	0.0564	0.3912	-8.0501	3.5225	11.4273
16	5.911	1.1504	-0.485	9.2009	-3.8247	9.0948	0.1627	-0.2208	-0.2809	0.4556	-0.6312	0.5008	0.2427	0.8511	0.7336	0.1703	-0.0297	0.0754	0.3021	-0.0084	0.3937	-9.9169	-0.5507	18.0048
17	6.6527	-0.103	4.0066	5.3764	3.5222	5.803	-0.419	-0.2025	0.1246	0.0578	-0.5612	0.3086	-0.2941	-0.623	1.0245	0.2528	-0.0333	0.0779	0.5182	-0.0112	0.532	-15.5436	1.8538	13.5634

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 16 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 43 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 44 through 55 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 56 through 80 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 81 through 85 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 16 through 39 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 40 through 87 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 15 through 42 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 43 through 77 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 78 through 86 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 17 through 34 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 35 through 43 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 44 through 48 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 49 through 53 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 54 through 62 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 63 through 77 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 78 through 86 )

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