PDB-3lw9: Structure of a Cytoplasmic Domain of Salmonella InvA

ID or keywords:

Entry

Database: PDB / ID: 3lw9

Title

Structure of a Cytoplasmic Domain of Salmonella InvA

Components

Invasion protein invA

Keywords

PROTEIN TRANSPORT / inva / type III secretion / salmonella / virulence / bacterial pathogenesis / Cell inner membrane / Cell membrane / Membrane / Transmembrane / Transport

Function / homology

Function and homology information

protein secretion / plasma membrane
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85 Å

Authors

Stebbins, C.E. / Lilic, M. / Quezada, C.M.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: A conserved domain in type III secretion links the cytoplasmic domain of InvA to elements of the basal body.
Authors: Lilic, M. / Quezada, C.M. / Stebbins, C.E.

History

Deposition	Feb 23, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 26, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Apr 11, 2012	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.4	Oct 13, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5	Nov 20, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3lw9.cif.gz	153.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3lw9.ent.gz	123.2 KB	Display	PDB format
PDBx/mmJSON format	3lw9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3lw9_validation.pdf.gz	431.5 KB	Display	wwPDB validaton report
Full document	3lw9_full_validation.pdf.gz	437.1 KB	Display
Data in XML	3lw9_validation.xml.gz	15.9 KB	Display
Data in CIF	3lw9_validation.cif.gz	22.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lw/3lw9 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/3lw9	HTTPS FTP

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Related structure data

Similar structure data	5j6z-d 2eea-d 1wg6-d 2noc-d 1wwa-2 3lru-d 3m1b-5 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: Invasion protein invA

B: Invasion protein invA

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

1

A: Invasion protein invA

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

2

B: Invasion protein invA

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

3

A: Invasion protein invA

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

4

B: Invasion protein invA

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

Unit cell

Length a, b, c (Å)	83.682, 83.682, 130.389
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

Details

Dimer in the asymmetric unit

#1: Protein	Invasion protein invA Mass: 19840.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: invA, STM2896 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A1I3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.88 Å³/Da / Density % sol: 57.24 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: For crystallization, InvA (356-525) was concentrated to 25mg/ml in a buffer containing 25mM Tris pH 8.0, 200mM NaCl, 2mM DTT. Crystals were grown by vapor diffusion using hanging drops ...Details: For crystallization, InvA (356-525) was concentrated to 25mg/ml in a buffer containing 25mM Tris pH 8.0, 200mM NaCl, 2mM DTT. Crystals were grown by vapor diffusion using hanging drops formed from mixing a 1:1 volume ratio of InvA (356-525) protein with an equilibration buffer consisting of 1.6M Ammonium sulfate, 0.1M MES pH 7.0, 8% Dioxane at 230C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal

Density Matthews: 2.88 Å³/Da / Density % sol: 57.24 %

Crystal grow

Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: For crystallization, InvA (356-525) was concentrated to 25mg/ml in a buffer containing 25mM Tris pH 8.0, 200mM NaCl, 2mM DTT. Crystals were grown by vapor diffusion using hanging drops ...

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Data collection

Diffraction

Mean temperature: 113 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 0.979 Å

Detector

Date: Mar 26, 2009

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Redundancy: 7.6 % / Av σ(I) over netI: 29.28 / Number: 573512 / R_merge(I) obs: 0.065 / Χ²: 1.04 / D res high: 1.85 Å / D res low: 50 Å / Num. obs: 75386 / % possible obs: 99.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
3.99	50	98.4	1	0.044	1.004	7.4
3.16	3.99	100	1	0.057	1.002	7.5
2.76	3.16	100	1	0.066	1.033	7.7
2.51	2.76	100	1	0.083	1.009	7.7
2.33	2.51	100	1	0.113	1.048	7.7
2.19	2.33	100	1	0.159	1.02	7.7
2.08	2.19	100	1	0.217	1.082	7.7
1.99	2.08	100	1	0.328	1.053	7.6
1.92	1.99	100	1	0.531	1.048	7.6
1.85	1.92	100	1	0.936	1.093	7.6

Reflection

Resolution: 1.85→50 Å / Num. obs: 75386 / % possible obs: 99.8 % / Redundancy: 7.6 % / R_merge(I) obs: 0.065 / Χ²: 1.039 / Net I/σ(I): 13.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.85-1.92	7.6	0.936	7608	1.093	1	100
1.92-1.99	7.6	0.531	7546	1.048	1	100
1.99-2.08	7.6	0.328	7525	1.053	1	100
2.08-2.19	7.7	0.217	7527	1.082	1	100
2.19-2.33	7.7	0.159	7553	1.02	1	100
2.33-2.51	7.7	0.113	7553	1.048	1	100
2.51-2.76	7.7	0.083	7513	1.009	1	100
2.76-3.16	7.7	0.066	7546	1.033	1	100
3.16-3.99	7.5	0.057	7607	1.002	1	100
3.99-50	7.4	0.044	7408	1.004	1	98.4

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	refmac_5.5.0044	refinement
PDB_EXTRACT	3.005	data extraction
SHELX		phasing
PHENIX		phasing
ARP		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.85→19.29 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.802 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.238	1863	5 %	RANDOM
R_work	0.21	-	-	-
obs	0.211	36968	100 %	-

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 max: 64.81 Å² / B_iso mean: 29.416 Å² / B_iso min: 13.23 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	-0.05 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→19.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2745	0	0	171	2916

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	2797
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	1909
X-RAY DIFFRACTION	r_angle_refined_deg	1.519	1.967	3783
X-RAY DIFFRACTION	r_angle_other_deg	0.937	3	4632
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.477	5	331
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.194	24.04	151
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.89	15	507
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.633	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	424
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3091
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	583
X-RAY DIFFRACTION	r_mcbond_it	0.823	1.5	1657
X-RAY DIFFRACTION	r_mcbond_other	0.244	1.5	670
X-RAY DIFFRACTION	r_mcangle_it	1.525	2	2688
X-RAY DIFFRACTION	r_scbond_it	2.915	3	1140
X-RAY DIFFRACTION	r_scangle_it	4.317	4.5	1095

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.307	126	-
R_work	0.238	2337	-
all	-	2463	-
obs	-	-	100 %

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	4.4754	0.6656	2.8486	4.2092	0.0175	5.3147	-0.1035	0.076	0.2859	-0.0186	0.1773	0.257	0.0519	-0.3783	-0.0737	0.0255	-0.0034	0.025	0.0646	0.0668	0.1273	-1.831	32.394	2.843
2	2.6112	-1.2325	-2.5545	6.8571	2.4195	11.9108	-0.1543	0.0212	0.2529	0.0408	0.0915	-0.137	-0.5554	-0.0782	0.0629	0.0778	0.0079	-0.0091	0.0034	0.0066	0.0938	6.534	37.674	2.184
3	6.2655	1.0131	0.938	11.0887	3.3628	6.2705	0.1373	-0.2649	0.1053	0.0705	-0.0545	0.2544	-0.0554	-0.3905	-0.0828	0.0661	-0.0188	0.0063	0.053	0.039	0.0961	5.964	27.263	-10.303
4	7.7229	0.1056	2.7561	1.6132	-0.2664	2.2814	-0.1476	-0.0922	0.4678	0.0716	0.126	0.19	-0.0302	-0.4763	0.0216	0.0452	0	0.0271	0.154	0.047	0.1022	-1.97	28.263	5.497
5	3.485	-2.2891	1.8251	3.6967	1.7628	12.5589	0.0452	0.0089	0.1332	-0.1808	-0.018	-0.3171	0.2927	0.4789	-0.0272	0.0404	0.0314	0.0309	0.0317	0.0151	0.0383	18.736	14.582	12.479
6	10.9531	0.9629	-0.4079	5.464	-0.1055	5.5687	-0.0297	0.1681	0.0951	-0.1315	0.0433	0.1098	0.0601	-0.0438	-0.0137	0.0214	0.0071	-0.0005	0.0072	0.0032	0.003	15.215	18.436	11.26
7	5.2875	1.7175	-5.218	13.1103	-1.5528	5.1511	0.054	-0.2588	0.1689	0.3482	0.1133	-0.5539	-0.0428	0.258	-0.1673	0.108	0.0271	0.0534	0.0224	-0.0014	0.082	20.788	17.273	5.173
8	10.6536	5.9445	4.7661	6.9767	3.5483	4.3421	0.1608	0.0869	0.106	0.239	-0.0555	0.1748	0.1573	-0.2029	-0.1053	0.0134	-0.0027	0.0073	0.0355	0.0253	0.0291	5.654	21.575	-0.484
9	6.2052	7.7155	3.7992	11.1599	4.9428	3.1084	0.0119	0.1916	-0.3321	-0.1081	0.0525	-0.0879	0.3017	0.2374	-0.0643	0.1706	-0.0056	-0.0115	0.2778	0.0211	0.1221	-10.19	7.342	-12.615
10	9.0947	-2.0939	5.0339	4.725	-2.4482	7.1801	-0.4145	-0.1907	-0.5064	-0.3674	0.2799	0.2994	0.219	0.0867	0.1346	0.2921	0.0363	-0.0039	0.1974	-0.0048	0.1517	-18.505	-11.401	-9.19
11	5.8853	-0.1603	4.8399	1.6366	-1.105	10.3875	-0.1312	0.2453	0.4592	-0.0834	0.1348	-0.0863	-0.8041	0.3167	-0.0037	0.1102	-0.0369	0.0319	0.0297	-0.006	0.1108	-0.858	32.183	37.939
12	1.4079	-0.5522	0.3421	1.6848	-4.3013	11.9638	0.0034	0.0013	0.0027	0.0114	-0.0187	0.0064	-0.1116	0.0266	0.0154	0.1185	0.0203	-0.0189	0.055	-0.0261	0.1194	-9.343	35.685	41.236
13	3.1875	1.977	-0.7256	3.0526	-1.6694	10.0245	-0.1058	-0.1819	0.4116	0.0063	-0.0151	-0.1495	-0.2033	0.2355	0.1209	0.0543	0.0326	-0.0265	0.0411	-0.0478	0.1519	-2.206	31.09	46.705
14	10.5536	1.0903	4.6578	0.5806	0.048	2.6154	-0.1289	0.2872	0.2104	-0.0942	0.0494	-0.0542	-0.0589	0.1449	0.0796	0.0613	-0.0223	0.0417	0.0175	-0.019	0.071	-1.099	25.215	35.377
15	2.982	0.6229	2.0001	2.6084	-1.5446	10.6831	-0.007	0.0245	0.0652	-0.0037	0.062	0.3051	0.4878	-0.3235	-0.0549	0.0311	-0.0191	0.0084	0.0143	0.0005	0.0398	-19.84	12.551	29.778
16	10.1232	0.14	-2.5869	5.7294	0.016	7.3603	-0.0516	-0.1259	-0.1706	0.0659	0.0203	-0.0266	-0.0063	-0.0036	0.0314	0.0011	0.001	0.0006	0.0018	0.0021	0.003	-16.258	16.961	31.101
17	6.0882	4.7843	-3.092	15.8473	0.7641	2.4212	-0.1521	0.0048	0.0664	-0.4153	0.042	0.5255	-0.0083	-0.0218	0.1102	0.0662	0.0614	-0.0017	0.1141	-0.0327	0.0718	-20.972	16.956	37.349
18	13.1636	-8.2882	8.5254	9.7029	-5.6547	5.5591	-0.144	-0.0398	0.0325	0.0445	0.1349	0.0199	-0.1253	-0.0163	0.0091	0.0621	-0.0298	0.0184	0.0168	-0.0084	0.0066	-7.509	21.701	42.924
19	9.0583	-7.8182	4.5972	10.7855	-4.9054	3.1072	-0.0044	-0.2079	-0.343	0.1609	0.0998	0.1375	0.2362	-0.0154	-0.0953	0.1426	0.0257	0.0197	0.0775	-0.0217	0.0646	8.403	8.221	53.984
20	7.9908	1.8398	5.7795	6.5356	4.7847	10.1388	-0.0858	-0.014	-0.2734	0.3643	0.1593	-0.1004	0.2603	0.2767	-0.0734	0.0412	0.0028	-0.0002	0.0724	0.0547	0.06	18.062	-10.142	50.882

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	358 - 370
2	X-RAY DIFFRACTION	2	A	371 - 381
3	X-RAY DIFFRACTION	3	A	382 - 395
4	X-RAY DIFFRACTION	4	A	396 - 428
5	X-RAY DIFFRACTION	5	A	429 - 446
6	X-RAY DIFFRACTION	6	A	447 - 469
7	X-RAY DIFFRACTION	7	A	470 - 475
8	X-RAY DIFFRACTION	8	A	476 - 491
9	X-RAY DIFFRACTION	9	A	492 - 508
10	X-RAY DIFFRACTION	10	A	509 - 523
11	X-RAY DIFFRACTION	11	B	359 - 370
12	X-RAY DIFFRACTION	12	B	371 - 385
13	X-RAY DIFFRACTION	13	B	386 - 406
14	X-RAY DIFFRACTION	14	B	407 - 429
15	X-RAY DIFFRACTION	15	B	430 - 446
16	X-RAY DIFFRACTION	16	B	447 - 469
17	X-RAY DIFFRACTION	17	B	470 - 476
18	X-RAY DIFFRACTION	18	B	477 - 490
19	X-RAY DIFFRACTION	19	B	491 - 508
20	X-RAY DIFFRACTION	20	B	509 - 525

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