PDB-6dhx: Structure of TipC2 from Streptococcus intermedius B196

ID or keywords:

Entry

Database: PDB / ID: 6dhx

Title

Structure of TipC2 from Streptococcus intermedius B196

Components

TipC2

Keywords

ANTITOXIN / Type VII secretion immunity protein

Function / homology

Uncharacterized protein

Function and homology information

Biological species

Streptococcus intermedius B196 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.75 Å

Authors

Bryant, D. / Klein, T.A. / Whitney, J.C.

Funding support

United States, 1items

Citation

Journal: J. Mol. Biol. / Year: 2018
Title: Molecular Basis for Immunity Protein Recognition of a Type VII Secretion System Exported Antibacterial Toxin.
Authors: Klein, T.A. / Pazos, M. / Surette, M.G. / Vollmer, W. / Whitney, J.C.

History

Deposition	May 21, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 24, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6dhx.cif.gz	246.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6dhx.ent.gz	205.9 KB	Display	PDB format
PDBx/mmJSON format	6dhx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dh/6dhx ftp://data.pdbj.org/pub/pdb/validation_reports/dh/6dhx	HTTPS FTP

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Related structure data

Similar structure data	6tkn-1 4mir-2 4die-4 4bfp-1 6h35-1 4aj0-1 3p0p-2 5hfg-d 1dae-d 3bhd-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) 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: TipC2

B: TipC2

C: TipC2

hetero molecules

70.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: TipC2

hetero molecules

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

2

B: TipC2

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

3

C: TipC2

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

Unit cell

Length a, b, c (Å)	159.740, 54.520, 104.430
Angle α, β, γ (deg.)	90.00, 108.05, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	TipC2 Mass: 23516.049 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus intermedius B196 (bacteria) Gene: SIR_1486 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1ZH71
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.32 Å³/Da / Density % sol: 62.95 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 100mM Tris-HCl pH 8.5, 25% w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.75→33.6 Å / Num. obs: 85866 / % possible obs: 99.2 % / Redundancy: 7.3 % / Net I/σ(I): 21.1
Reflection shell	Resolution: 1.75→1.78 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
xia2		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.75→33.6 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.99

	R_factor	Num. reflection	% reflection
R_free	0.1943	1947	2.32 %
R_work	0.1699	-	-
obs	0.1705	83810	96.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.75→33.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4484	0	5	489	4978

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	4591
X-RAY DIFFRACTION	f_angle_d	1.221	6211
X-RAY DIFFRACTION	f_dihedral_angle_d	12.622	2755
X-RAY DIFFRACTION	f_chiral_restr	0.086	665
X-RAY DIFFRACTION	f_plane_restr	0.007	780

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 (%)
1.75-1.7938	0.2869	130	0.2901	5381	X-RAY DIFFRACTION	90
1.7938-1.8423	0.3002	125	0.257	5467	X-RAY DIFFRACTION	91
1.8423-1.8965	0.2145	136	0.2213	5567	X-RAY DIFFRACTION	93
1.8965-1.9577	0.226	130	0.1924	5698	X-RAY DIFFRACTION	95
1.9577-2.0276	0.2323	141	0.1727	5785	X-RAY DIFFRACTION	97
2.0276-2.1088	0.1986	140	0.1649	5882	X-RAY DIFFRACTION	97
2.1088-2.2048	0.2062	141	0.1589	5886	X-RAY DIFFRACTION	98
2.2048-2.321	0.2054	140	0.1587	5940	X-RAY DIFFRACTION	98
2.321-2.4664	0.1919	142	0.1624	5953	X-RAY DIFFRACTION	99
2.4664-2.6567	0.2031	143	0.1688	5990	X-RAY DIFFRACTION	99
2.6567-2.9239	0.204	144	0.1772	6017	X-RAY DIFFRACTION	100
2.9239-3.3467	0.1886	145	0.1661	6067	X-RAY DIFFRACTION	100
3.3467-4.2152	0.1658	144	0.1506	6065	X-RAY DIFFRACTION	99
4.2152-33.6063	0.1871	146	0.1703	6165	X-RAY DIFFRACTION	99

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	2.9556	-0.2524	-0.0249	1.0331	0.4407	1.2338	-0.0277	-0.0655	0.2255	0.2791	-0.3274	-0.7023	-0.4076	0.7691	0.0134	0.2688	-0.093	-0.0384	0.2306	0.0523	0.2683	38.3113	1.7414	24.6815
2	3.2169	-0.217	0.6605	2.8275	-0.1034	3.3038	-0.2297	-0.22	0.1456	0.5771	0.011	-0.0587	-0.5377	-0.0145	0.1566	0.3665	-0.0358	0.0185	0.1519	-0.0166	0.1507	27.6814	-2.7074	33.8394
3	5.8692	-2.4915	-0.7173	4.8816	-0.2108	2.5682	-0.1768	0.3982	-0.9463	-0.1019	-0.2564	0.0683	0.6436	0.2851	0.2429	0.4499	0.0208	0.1231	0.2315	-0.0063	0.3522	30.2937	-16.1798	29.4635
4	0.8195	-0.0363	-0.2428	1.6502	-0.2588	2.5002	-0.0384	0.1586	-0.2711	0.1111	-0.1828	0.3385	-0.0124	-0.29	0.1773	0.2153	-0.0165	0.046	0.2308	-0.086	0.2815	22.6153	-8.0489	21.1143
5	7.0539	1.5507	1.4041	1.4177	0.2212	1.1905	0.2173	0.3609	-0.4386	0.0615	-0.209	0.2421	0.2953	-0.3276	0.1199	0.2188	-0.0496	-0.0053	0.3601	-0.1092	0.28	21.1045	-9.4304	12.5278
6	0.887	-0.5408	-0.5014	0.833	-0.5365	1.492	-0.0074	0.456	-0.26	-0.0189	-0.1668	0.1519	0.2487	-0.1494	0.1083	0.1834	-0.0138	0.0484	0.3061	-0.1005	0.2189	27.5361	-8.1682	11.663
7	1.9229	-0.2404	-0.4533	2.7728	1.0661	1.4068	-0.1309	-0.1245	-0.0134	0.1201	-0.2277	0.4279	-0.0221	-0.4529	-1.0052	0.2715	0.0715	-0.0497	0.5491	-0.1993	0.3258	15.6747	-13.7437	4.4285
8	3.338	0.4893	1.0593	2.1417	1.2604	4.3156	0.0331	0.4533	0.0081	-0.6066	-0.37	0.6033	-0.8422	-0.2917	0.1341	0.385	0.1074	-0.0856	0.3663	-0.0844	0.2831	17.6761	1.8571	9.3012
9	2.9218	-0.597	-1.0964	1.6562	0.3005	2.7027	-0.0322	0.2816	0.4858	0.1548	-0.1566	0.0189	-0.7921	-0.1167	0.032	0.3489	0.0047	-0.0272	0.1842	0.0193	0.2375	27.8038	7.2315	21.1924
10	7.8691	3.2722	5.2095	2.0852	2.3775	3.5176	-0.2541	0.8102	0.4498	-0.9653	-0.2798	0.2223	-0.4939	0.1316	0.2142	0.4071	0.0119	-0.022	0.5069	-0.043	0.2395	26.8873	-1.8803	2.7355
11	2.376	0.0395	-0.1772	1.3797	-0.4091	1.8918	-0.0145	0.5826	0.4499	-0.2513	0.0926	0.0791	-0.12	-0.2968	0.011	0.2619	0.0067	-0.0521	0.2661	0.0663	0.2933	9.0745	21.6759	28.6642
12	3.1667	-0.7022	0.6326	0.5542	0.0479	3.6966	-0.0675	-0.1289	0.1832	0.0769	0.105	0.2631	-0.1071	-0.4073	0.0267	0.2185	0.0185	-0.0118	0.1767	-0.0067	0.2757	8.4111	17.1416	43.2512
13	3.0143	-0.0992	-1.2876	1.0623	-0.3569	1.8905	0.1418	0.2001	-0.0552	-0.1028	-0.2385	0.3943	0.1308	-0.3849	0.0519	0.3245	0.0623	-0.0149	0.2692	-0.0162	0.2502	15.1033	11.2652	58.7785
14	1.6386	0.0961	-1.1027	2.1211	-0.2189	2.182	-0.0367	0.0258	0.0498	0.0058	-0.0525	-0.1281	0.1019	0.395	0.0562	0.2456	0.0059	0.0124	0.1816	-0.0039	0.2286	21.0527	13.6044	37.5503
15	0.5004	-0.1488	-0.2146	1.5105	0.3501	2.2449	-0.0444	0.4807	-0.0868	-0.8395	0.0155	-0.1093	0.7237	0.0896	0.0743	0.3122	0.0058	0.0605	0.4082	0.0255	0.3075	55.4021	-7.3733	2.7877
16	2.044	-0.0624	0.0623	2.8881	-0.4303	3.3201	-0.2743	0.3039	0.5419	-0.0869	0.0645	-0.3859	-0.2841	0.4305	-0.0344	0.2393	-0.0169	-0.0049	0.4178	0.1253	0.3565	59.5436	7.3688	6.6328
17	2.0708	-0.1145	0.8698	2.0598	-0.4168	2.0045	-0.0745	0.0235	0.0899	0.0672	0.0479	-0.5423	-0.1116	0.6395	-0.0957	0.1969	0.0152	-0.0108	0.3852	0.0794	0.321	63.3165	0.0521	17.8504
18	0.8265	-0.1318	-0.0068	1.581	-0.5259	0.6994	-0.1047	0.1319	-0.1387	-0.1458	0.2067	-0.6365	-0.1375	0.7818	-0.1887	0.2311	0.0441	0.0007	0.3583	0.0524	0.3402	65.7908	-5.6789	18.7017
19	0.7204	-0.6972	0.1295	3.2558	0.987	0.5918	-0.1717	-0.4893	0.4703	-0.3527	0.3279	-0.6285	-0.3714	-0.393	0.2203	0.2624	0.1068	-0.1287	0.6017	0.1275	0.3214	70.1454	-1.3219	31.7085
20	3.0096	0.2608	0.1147	1.457	-0.0555	2.018	0.0049	-0.2754	-0.3541	0.0638	0.0443	-0.1509	0.3784	-0.0351	0.1045	0.238	-0.0105	0.0032	0.3088	0.0716	0.288	53.462	-8.0861	18.3981

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 22 through 40 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 41 through 52 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 53 through 66 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 107 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 108 through 119 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 120 through 135 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 136 through 158 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 159 through 169 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 170 through 194 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 195 through 203 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 24 through 52 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 53 through 135 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 136 through 158 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 159 through 203 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 23 through 40 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 41 through 81 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 82 through 119 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 120 through 135 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 136 through 158 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 159 through 203 )

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