PDB-6b12: Structure of Tne2 in complex with Tni2

ID or keywords:

Entry

Database: PDB / ID: 6b12

Title

Structure of Tne2 in complex with Tni2

Components

Tne2
Tni2

Keywords

ANTIMICROBIAL PROTEIN / type VI secretion / effector / immunity / NADase / toxin

Function / homology

PAAR motif / PAAR motif / membrane / Uncharacterized protein / PAAR motif containing protein

Function and homology information

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.71 Å

Authors

Tang, J.Y. / Whitney, J.C.

Funding support

Canada, 1items

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Diverse NADase effector families mediate interbacterial antagonism via the type VI secretion system.
Authors: Tang, J.Y. / Bullen, N.P. / Ahmad, S. / Whitney, J.C.

History

Deposition	Sep 15, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 27, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Feb 21, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 30, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6b12.cif.gz	239.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6b12.ent.gz	193.3 KB	Display	PDB format
PDBx/mmJSON format	6b12.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6b12_validation.pdf.gz	446.2 KB	Display	wwPDB validaton report
Full document	6b12_full_validation.pdf.gz	448 KB	Display
Data in XML	6b12_validation.xml.gz	27.2 KB	Display
Data in CIF	6b12_validation.cif.gz	40.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b1/6b12 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/6b12	HTTPS FTP

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Related structure data

Similar structure data	1h5f-d 5dt4-d 3h10-2 2g07-1 5os2-d 4r74-2 3h10-1 2hk7-1 1h5k-d 7l0g-2 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: Tne2

B: Tni2

C: Tni2

D: Tne2

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

1

A: Tne2

C: Tni2

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

2

B: Tni2

D: Tne2

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

Unit cell

Length a, b, c (Å)	176.690, 40.560, 95.910
Angle α, β, γ (deg.)	90.00, 97.24, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-597- HOH

#1: Protein	Tne2 / PAAR motif containing protein Mass: 14784.232 Da / Num. of mol.: 2 / Fragment: UNP residues 290-408 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria) Gene: PFL_6209 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus / References: UniProt: Q4K3B6
#2: Protein	Tni2 Mass: 17792.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria) Gene: PFL_6210 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus / References: UniProt: Q4K3B5
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 574 / 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: 2.65 Å³/Da / Density % sol: 53.53 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 34% (v/v) PEG 400, 100 mM MgCl2, 100 mM MES-NaOH pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 12, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.71→68.94 Å / Num. obs: 72673 / % possible obs: 98.7 % / Redundancy: 2 % / Net I/σ(I): 13.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.71→68.936 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.99

	R_factor	Num. reflection	% reflection
R_free	0.2163	3572	4.92 %
R_work	0.1814	-	-
obs	0.1831	72666	98.64 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.71→68.936 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4236	0	0	574	4810

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4322
X-RAY DIFFRACTION	f_angle_d	0.893	5878
X-RAY DIFFRACTION	f_dihedral_angle_d	12.408	2590
X-RAY DIFFRACTION	f_chiral_restr	0.064	662
X-RAY DIFFRACTION	f_plane_restr	0.006	774

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 (%)
1.71-1.7325	0.3941	119	0.3775	2266	X-RAY DIFFRACTION	86
1.7325-1.7562	0.4395	135	0.3676	2410	X-RAY DIFFRACTION	90
1.7562-1.7813	0.3739	117	0.3309	2553	X-RAY DIFFRACTION	94
1.7813-1.8079	0.3198	119	0.2811	2592	X-RAY DIFFRACTION	98
1.8079-1.8362	0.2972	158	0.2559	2673	X-RAY DIFFRACTION	100
1.8362-1.8663	0.2635	155	0.2233	2646	X-RAY DIFFRACTION	100
1.8663-1.8985	0.236	136	0.2117	2665	X-RAY DIFFRACTION	100
1.8985-1.933	0.2274	134	0.1953	2703	X-RAY DIFFRACTION	100
1.933-1.9702	0.2247	134	0.1906	2621	X-RAY DIFFRACTION	100
1.9702-2.0104	0.2155	139	0.177	2690	X-RAY DIFFRACTION	100
2.0104-2.0541	0.2488	122	0.1782	2657	X-RAY DIFFRACTION	99
2.0541-2.1019	0.2099	117	0.1762	2717	X-RAY DIFFRACTION	100
2.1019-2.1545	0.2043	147	0.1729	2679	X-RAY DIFFRACTION	100
2.1545-2.2127	0.1728	133	0.1764	2680	X-RAY DIFFRACTION	100
2.2127-2.2778	0.2498	150	0.1769	2659	X-RAY DIFFRACTION	100
2.2778-2.3514	0.2409	136	0.179	2653	X-RAY DIFFRACTION	100
2.3514-2.4354	0.2364	132	0.1783	2704	X-RAY DIFFRACTION	100
2.4354-2.5329	0.2024	168	0.1728	2680	X-RAY DIFFRACTION	100
2.5329-2.6482	0.2036	132	0.1766	2676	X-RAY DIFFRACTION	100
2.6482-2.7878	0.1926	144	0.1789	2690	X-RAY DIFFRACTION	100
2.7878-2.9625	0.2035	138	0.1875	2720	X-RAY DIFFRACTION	100
2.9625-3.1912	0.2064	152	0.1818	2681	X-RAY DIFFRACTION	100
3.1912-3.5124	0.21	141	0.1692	2712	X-RAY DIFFRACTION	100
3.5124-4.0206	0.1974	143	0.1576	2746	X-RAY DIFFRACTION	100
4.0206-5.0653	0.1772	134	0.1414	2771	X-RAY DIFFRACTION	100
5.0653-68.9918	0.2114	137	0.1842	2850	X-RAY DIFFRACTION	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	1.7038	0.3983	0.0585	0.759	0.1868	1.0444	-0.0385	-0.3251	-0.0534	0.1867	-0.0535	0.1683	-0.0253	-0.3631	0.053	0.1664	0.0263	0.0326	0.3536	-0.0064	0.2443	4.3531	-4.3136	105.3101
2	2.6437	0.0504	-0.2084	1.4127	0.6207	2.8681	-0.087	-0.2108	0.2151	0.0332	-0.0813	0.0282	-0.1574	-0.0677	0.1717	0.1736	0.029	0.0108	0.3807	-0.0063	0.2749	1.3922	-0.9267	102.3102
3	1.0795	-0.0338	1.0801	1.0338	0.2157	1.6306	0.0165	-0.0038	0.0786	-0.5501	0.0372	0.4036	-0.3785	-0.4454	-0.0073	0.5108	0.0615	-0.0536	0.2241	-0.0035	0.271	18.4823	20.8194	62.0809
4	0.8087	0.1411	-0.2054	1.0553	-0.3576	1.6133	-0.0063	0.0101	0.038	-0.4206	0.0034	-0.0661	-0.1138	0.166	-0.0122	0.2821	0.0008	0.0201	0.1466	-0.0075	0.1706	28.5217	14.0138	66.9612
5	1.355	-0.0238	-0.2624	0.0516	0.1226	1.998	0.215	0.2295	-0.0913	-0.6472	0.2648	-0.6146	-0.0244	0.7275	0.0255	0.468	0.0044	0.1038	0.2241	-0.0552	0.2096	33.7973	7.9033	60.3486
6	1.3745	-1.2088	-0.8923	2.787	0.8099	0.9186	-0.2569	-0.0176	-0.1818	-0.3251	0.196	0.0342	0.4324	-0.0154	0.0428	0.6115	0.0365	0.014	0.2281	-0.0306	0.2324	27.4816	-2.3561	51.7302
7	0.8453	-0.137	0.4237	0.5757	0.6616	2.6713	0.1408	0.1435	0.0647	-0.628	0.1009	0.1346	0.0426	-0.1713	-0.0399	0.5662	-0.0011	-0.0577	0.1642	0.0031	0.2176	21.8384	-0.7934	56.3428
8	2.0518	0.634	1.0425	0.5791	1.6552	5.3909	-0.1518	0.1508	0.2827	-0.6773	-0.1644	0.2614	0.0796	-0.1445	0.1949	0.4982	0.0193	-0.0444	0.1469	0.012	0.2087	24.2082	-2.3067	59.9698
9	4.2023	0.331	0.2428	2.1428	-2.4679	4.9945	0.0489	0.5295	0.3252	-0.3231	0.2886	0.4572	1.1227	-0.5835	-0.184	0.6916	0.0201	-0.0823	0.3132	0.037	0.2733	22.1083	-5.8877	56.2392
10	1.8066	0.5718	-0.7501	1.0418	0.632	0.9855	-0.013	0.1245	0.0288	-0.1162	0.0146	0.4487	0.1769	-0.4168	0.0258	0.2013	-0.0156	-0.0217	0.2068	-0.017	0.2952	14.9755	-16.6627	86.9371
11	0.1524	-0.1786	-0.044	1.1982	-0.642	2.1911	-0.0069	-0.0085	-0.0257	-0.1404	0.0227	-0.1104	0.1994	0.2094	-0.005	0.1296	0.0125	-0.0014	0.1505	-0.0159	0.1888	26.9156	-12.7381	84.748
12	0.6127	0.1512	0.002	1.1926	0.067	2.0916	0.0029	-0.0943	-0.0169	0.0697	-0.0111	-0.0587	0.0995	0.0218	0.0248	0.1161	0.0131	-0.012	0.1334	-0.0025	0.1676	25.3449	-4.9761	91.2315
13	1.769	-0.905	-0.9847	4.3853	3.8086	6.2577	0.1682	-0.1143	0.3368	-0.0139	0.3193	-0.5304	-0.2589	0.5533	-0.3203	0.1317	-0.0073	-0.0044	0.1752	-0.0425	0.2492	32.0832	-1.687	87.6196
14	1.2034	0.6653	0.4728	3.0638	0.4722	1.468	-0.0177	0.0145	0.0733	0.3105	0.1752	-0.0971	-0.3169	0.0518	-0.1782	0.2002	0.0002	0.0185	0.1561	-0.0203	0.1884	20.9216	6.8587	99.5824
15	1.3877	-0.0867	-0.434	1.2517	0.3768	2.8676	0.1636	-0.072	0.0586	0.1075	0.0926	0.1861	0.0158	-0.1717	-0.2062	0.1264	0.0105	0.0202	0.1414	-0.0012	0.2072	16.6962	4.9354	93.3517
16	2.2559	-0.463	-1.1797	1.4089	0.8093	3.3745	-0.1096	-0.3142	-0.1319	0.0871	-0.0381	0.2581	0.3786	-0.0519	0.0489	0.1888	0.0007	-0.0046	0.1913	-0.0226	0.24	19.9604	6.43	90.4775
17	6.6658	1.828	-2.2418	3.9657	-1.1492	5.1731	0.2194	-0.225	-0.1964	0.5682	-0.0199	0.4152	-0.3972	-0.2025	-0.1629	0.274	-0.0082	0.064	0.1729	0.0141	0.2634	17.0316	9.9658	93.5785
18	3.4334	0.8788	0.2005	2.0359	-0.3654	0.1073	-0.1993	0.2307	0.0176	-0.5708	-0.2577	0.2524	0.5353	-0.1571	0.0243	0.5977	-0.2136	0.0843	0.6515	-0.3056	0.392	6.8837	-6.637	33.5928
19	2.4354	0.2205	-0.1541	5.9125	1.5999	1.0488	-0.2844	0.4975	-0.3214	-0.4537	-0.0346	0.1902	-0.224	-0.019	0.3896	0.447	-0.1605	0.005	0.6815	-0.0109	0.23	15.6285	7.1817	29.3681
20	1.3781	0.3603	0.151	0.6452	-0.0589	1.619	-0.3281	0.2519	0.1035	-0.0792	0.1118	-0.0283	-0.1915	-0.3967	0.1978	0.4998	-0.0443	-0.0374	0.3126	-0.0124	0.2195	14.9944	10.8304	48.1375
21	2.4251	0.0006	-1.6014	2.2129	0.4801	3.3167	-0.1855	0.6474	-0.4367	-0.285	-0.1867	0.5352	0.0754	-0.2957	0.3958	0.3838	-0.0645	-0.0034	0.5262	-0.027	0.2505	1.0668	6.4957	44.7719
22	1.6896	0.5753	1.1197	3.3042	0.7299	5.0219	-0.1205	-0.0644	-0.3669	0.5093	0.0738	-0.2376	0.2127	-0.6563	0.0829	0.4372	-0.0689	0.0613	0.3734	-0.0274	0.312	6.6403	1.4171	51.056
23	1.7	-0.6798	-0.0577	1.1353	0.6643	1.4893	-0.2206	0.3878	-0.179	0.0334	-0.1157	0.2543	-0.0581	-0.1587	0.2791	0.4143	-0.1848	0.0423	0.4476	-0.0516	0.209	9.6346	3.4441	40.0955
24	7.9702	0.0606	-1.1958	3.3435	-0.0224	1.4148	0.0349	0.2039	-0.2076	0.0639	-0.1501	0.3344	0.5202	-0.3051	0.1183	0.4312	-0.182	0.0616	0.5594	-0.0837	0.2257	12.4777	2.2349	37.0585
25	3.5334	-0.01	-1.2423	5.5087	1.4001	5.1185	0.2015	0.3024	-0.1154	-0.1672	0.0816	-0.664	-0.4057	0.6059	-0.1689	0.4834	-0.1866	-0.0634	0.5221	0.0345	0.2739	20.3294	11.1561	40.2326
26	1.1447	-1.0587	0.7459	1.5444	0.4464	2.7005	0.0392	-0.5699	0.0876	0.1618	-0.1039	0.0512	-0.2126	-0.3591	-0.0309	0.5013	0.0166	-0.0564	0.3524	-0.0351	0.3308	3.0897	13.9811	50.8604

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 293 through 338 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 339 through 408 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 33 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 34 through 70 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 71 through 95 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 96 through 112 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 113 through 133 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 134 through 144 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 145 through 153 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 33 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 34 through 58 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 59 through 84 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 85 through 95 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 96 through 112 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 113 through 133 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 134 through 144 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 145 through 153 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 290 through 297 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 298 through 306 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 307 through 332 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 333 through 344 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 345 through 357 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 358 through 385 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 386 through 391 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 392 through 399 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 400 through 408 )

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+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi