PDB-6a7h: Bacterial protein toxins

ID or keywords:

Entry

Database: PDB / ID: 6a7h

Title

Bacterial protein toxins

Components

RTX toxin

Keywords

TOXIN / protein toxins / virulence

Function / homology

Function and homology information

host cell membrane / toxin activity / extracellular region / membrane
Similarity search - Function

Biological species

Vibrio vulnificus CMCP6 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.301 Å

Authors

Kim, M.H. / Hwang, J. / Jang, S.Y.

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Structural basis of inactivation of Ras and Rap1 small GTPases by Ras/Rap1-specific endopeptidase from the sepsis-causing pathogenVibrio vulnificus
Authors: Jang, S.Y. / Hwang, J. / Kim, B.S. / Lee, E.Y. / Oh, B.H. / Kim, M.H.

History

Deposition	Jul 3, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 10, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 17, 2018	Group: Data collection / Database references / Structure summary Category: citation / citation_author / entity 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 / _entity.formula_weight
Revision 1.2	Dec 5, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Mar 27, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6a7h.cif.gz	755.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6a7h.ent.gz	627.2 KB	Display	PDB format
PDBx/mmJSON format	6a7h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6a7h_validation.pdf.gz	464 KB	Display	wwPDB validaton report
Full document	6a7h_full_validation.pdf.gz	474.5 KB	Display
Data in XML	6a7h_validation.xml.gz	74.2 KB	Display
Data in CIF	6a7h_validation.cif.gz	108.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a7/6a7h ftp://data.pdbj.org/pub/pdb/validation_reports/a7/6a7h	HTTPS FTP

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Related structure data

Related structure data	6a8jC C: citing same article (ref.)
Similar structure data	6a8j-1 6a8j-4 3ly6-2 1nug-1 6a8j-2 1nuf-d 6a8p-3 1nud-2 310 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

Related structure data

6a8jC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: RTX toxin

B: RTX toxin

C: RTX toxin

D: RTX toxin

hetero molecules

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

1

A: RTX toxin

hetero molecules

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

2

B: RTX toxin

hetero molecules

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

3

C: RTX toxin

hetero molecules

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

4

D: RTX toxin

hetero molecules

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

Unit cell

Length a, b, c (Å)	178.541, 198.279, 164.023
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-4277- HOH
2	1	A-4448- HOH
3	1	C-4240- HOH
4	1	C-4393- HOH

#1: Protein	RTX toxin Mass: 52978.582 Da / Num. of mol.: 4 / Mutation: E3930L,H4030L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus CMCP6 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSN9*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1099 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	The sequence has been deposited to database with accession number WP_011081430. N-terminal residues ...The sequence has been deposited to database with accession number WP_011081430. N-terminal residues GAMA are from expression tag. And protein used in this structure contains mutations E3930L,H4030L.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.43 Å³/Da / Density % sol: 64.09 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M LiSO4, 28% PEG4000, 0.1 M Tris-HCl (pH 8.0)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 128159 / % possible obs: 99.9 % / Redundancy: 6.6 % / Net I/σ(I): 19.87
Reflection shell	Resolution: 2.3→2.34 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.301→34.88 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.24 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2303	6422	5.02 %
R_work	0.1784	-	-
obs	0.181	127949	99.76 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.301→34.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14576	0	45	1099	15720

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	14850
X-RAY DIFFRACTION	f_angle_d	1.038	20051
X-RAY DIFFRACTION	f_dihedral_angle_d	14.56	5481
X-RAY DIFFRACTION	f_chiral_restr	0.039	2236
X-RAY DIFFRACTION	f_plane_restr	0.004	2621

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 (%)
2.3013-2.3275	0.3173	218	0.2427	3874	X-RAY DIFFRACTION	98
2.3275-2.3548	0.3413	205	0.239	4034	X-RAY DIFFRACTION	100
2.3548-2.3835	0.2971	225	0.2372	4025	X-RAY DIFFRACTION	100
2.3835-2.4137	0.2943	212	0.2271	3997	X-RAY DIFFRACTION	100
2.4137-2.4455	0.2608	221	0.222	4047	X-RAY DIFFRACTION	100
2.4455-2.479	0.2709	196	0.2146	4021	X-RAY DIFFRACTION	100
2.479-2.5144	0.2687	220	0.2195	4037	X-RAY DIFFRACTION	100
2.5144-2.5519	0.2829	202	0.2174	4017	X-RAY DIFFRACTION	100
2.5519-2.5917	0.2849	210	0.213	4015	X-RAY DIFFRACTION	100
2.5917-2.6342	0.2856	209	0.2253	4040	X-RAY DIFFRACTION	100
2.6342-2.6796	0.2578	206	0.2109	4065	X-RAY DIFFRACTION	100
2.6796-2.7283	0.2811	195	0.2063	4031	X-RAY DIFFRACTION	100
2.7283-2.7808	0.2744	228	0.2025	4045	X-RAY DIFFRACTION	100
2.7808-2.8375	0.2608	207	0.207	4047	X-RAY DIFFRACTION	100
2.8375-2.8992	0.2828	203	0.2131	4048	X-RAY DIFFRACTION	100
2.8992-2.9666	0.2886	212	0.2167	4031	X-RAY DIFFRACTION	100
2.9666-3.0407	0.314	215	0.218	4043	X-RAY DIFFRACTION	100
3.0407-3.1229	0.2899	202	0.2089	4031	X-RAY DIFFRACTION	100
3.1229-3.2147	0.2462	210	0.1993	4087	X-RAY DIFFRACTION	100
3.2147-3.3184	0.2694	228	0.1944	4040	X-RAY DIFFRACTION	100
3.3184-3.4369	0.2469	181	0.1889	4098	X-RAY DIFFRACTION	100
3.4369-3.5744	0.2269	209	0.1743	4079	X-RAY DIFFRACTION	100
3.5744-3.7369	0.2044	204	0.1574	4064	X-RAY DIFFRACTION	100
3.7369-3.9337	0.2067	255	0.1478	4025	X-RAY DIFFRACTION	100
3.9337-4.1798	0.17	240	0.1302	4058	X-RAY DIFFRACTION	100
4.1798-4.5019	0.1576	220	0.1254	4074	X-RAY DIFFRACTION	100
4.5019-4.9538	0.1643	209	0.126	4099	X-RAY DIFFRACTION	100
4.9538-5.6679	0.2166	239	0.1595	4079	X-RAY DIFFRACTION	100
5.6679-7.131	0.2333	210	0.1783	4170	X-RAY DIFFRACTION	100
7.131-34.8842	0.1637	231	0.1558	4206	X-RAY DIFFRACTION	98

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	8.218	-1.166	2.7693	0.1442	-0.0737	0.9244	0.6088	0.7967	-0.6631	-0.1757	0.0213	0.0755	-0.0055	0.1105	-0.6276	0.3471	0.0453	0.0012	0.6661	-0.0281	0.5089	-84.4734	41.7928	0.4794
2	4.8427	0.8635	-0.2476	2.662	0.5997	2.5562	0.1148	0.383	-0.1242	-0.4114	-0.1329	0.3931	-0.3817	-0.4268	-0.0023	0.3018	0.0834	-0.0038	0.2682	-0.0361	0.281	-62.9956	46.1105	4.6208
3	1.0014	0.4419	1.0485	4.7557	1.8566	3.1331	0.004	-0.0014	-0.1341	-0.2211	-0.1542	0.3957	-0.1457	-0.2202	0.1521	0.2461	0.0314	0.0522	0.3405	-0.035	0.3177	-51.4605	34.9228	1.4843
4	4.6438	-1.4818	0.0169	5.2115	0.0382	3.495	0.0627	0.157	0.1333	-0.1437	-0.1638	0.4573	0.0716	-0.269	0.0941	0.2813	-0.0251	-0.0142	0.2287	-0.0294	0.2105	-51.7778	15.3178	-10.978
5	2.9576	2.8825	4.3235	2.9977	4.4884	6.5421	0.6102	-0.2705	-0.0009	0.646	-0.3662	0.2134	0.3509	-0.1772	-0.1667	0.3174	-0.0003	0.0249	0.3018	-0.0469	0.3709	-44.9099	33.6361	6.9286
6	2.6407	0.9542	0.3127	4.9286	0.7645	1.1154	0.1451	0.0145	-0.2599	0.3206	0.0695	-1.0319	0.0954	0.383	-0.1816	0.2912	0.0145	-0.0687	0.3306	0.0025	0.4006	-17.3811	21.8693	9.505
7	2.1738	0.7688	0.3778	3.7286	1.1744	4.8172	0.1237	-0.0287	-0.0811	0.2391	-0.0645	-0.225	0.1429	-0.0496	-0.0407	0.3644	0.0065	-0.0232	0.2191	0.0271	0.2909	-33.8759	7.3781	4.907
8	7.7847	-3.338	3.2093	6.5442	-3.1629	2.7721	0.1426	0.7002	-0.0196	-0.7534	-0.1434	-0.2937	0.6846	-0.156	0.0086	0.4082	-0.0153	0.1046	0.3195	-0.0865	0.2815	-36.6173	28.892	0.992
9	4.5086	-1.6973	1.5265	7.5665	-1.0758	1.3362	0.1252	0.159	0.1595	0.0395	-0.0458	-0.7452	-0.166	0.2885	-0.0574	0.3089	-0.0495	0.0019	0.2649	-0.0454	0.3208	-22.927	27.5948	6.8456
10	5.3766	0.1945	-1.3932	-0.9949	-0.6413	-0.1523	0.1882	-0.3012	0.4254	-0.0008	-0.0382	0.3762	-0.0251	-0.3015	-0.1427	0.3259	-0.0323	0.0567	0.5457	-0.0996	0.7624	-74.1339	56.9618	-40.0255
11	0.7245	-0.1947	0.0852	4.0856	1.3389	1.1746	0.0424	0.0402	-0.1477	0.3008	-0.1984	0.421	0.0067	-0.2356	0.1468	0.2314	-0.0157	0.0566	0.294	-0.0069	0.2839	-53.2014	78.5252	-33.7902
12	0.7845	-0.8479	-0.2565	3.7033	0.7781	0.9621	0.1701	0.0523	0.018	-0.2202	-0.1389	-0.7357	-0.1104	0.1927	-0.0151	0.2617	-0.0054	0.0773	0.3408	0.0411	0.3886	-28.9324	80.3758	-48.5577
13	6.7173	0.9606	-3.8084	-0.3986	-0.2586	1.0592	-0.0136	0.5768	0.0598	0.0938	0.0766	-0.0088	0.0384	-0.1186	-0.1094	0.3064	-0.02	0.0613	0.5466	0.0058	0.3796	-5.0038	54.0851	-7.0958
14	0.3659	-0.6808	0.4849	3.1252	-1.3024	0.5777	-0.0508	0.0524	-0.0142	-0.1808	-0.0591	-0.1674	0.0145	0.0549	0.1209	0.3834	-0.0021	0.0734	0.3036	0.0142	0.2487	-32.2124	72.2842	-5.4801
15	1.0629	0.7974	-0.1191	4.0711	-0.6034	1.1012	0.0495	-0.0556	-0.005	0.1303	-0.0341	0.3936	-0.03	-0.1546	-0.0092	0.3011	0.0203	0.0466	0.249	-0.004	0.2063	-55.4342	78.1654	10.6629
16	2.7039	0.0922	1.0087	0.2463	-0.0452	0.5267	0.4723	-0.2641	-0.0777	0.0924	-0.1335	0.0565	0.1049	0.0638	-0.2041	0.2987	-0.0128	-0.0178	0.6244	-0.0251	0.438	-0.1485	44.2107	-36.7808
17	5.0508	-0.9626	0.854	1.9668	-0.2811	2.3514	0.2389	-0.332	0.1781	0.1776	-0.1823	-0.2495	-0.1819	0.3912	-0.0685	0.2043	-0.0559	-0.0145	0.3295	0.0043	0.2882	-21.8991	48.2779	-41.3877
18	0.6391	-1.2615	0.6665	6.6073	-1.8266	2.9739	-0.1088	-0.1336	-0.0475	0.4328	-0.0909	-0.3266	-0.0404	0.0737	0.2011	0.1037	-0.0505	0.0164	0.3231	0.0481	0.3029	-33.7854	37.1925	-40.3323
19	4.1017	1.2444	-0.2096	4.9867	-0.0564	2.9387	0.0082	-0.1124	0.122	0.3775	-0.1545	-0.3161	-0.0526	0.2507	0.1384	0.2661	0.0176	-0.0374	0.2184	0.0294	0.2044	-35.2396	17.4857	-28.267
20	2.076	0	0.9874	2.9241	-0.3342	1.3841	0.1077	0.134	-0.107	-0.5354	-0.099	0.72	0.0291	-0.2666	0.0007	0.3347	0.0406	-0.1032	0.4021	-0.0561	0.4493	-59.4071	32.7944	-51.9587
21	8.2799	0.522	-0.8357	3.9718	-2.8766	3.822	0.2418	-0.0601	-0.3838	-0.3826	-0.0482	1.1005	0.1759	-0.3681	-0.0947	0.3271	0.0009	-0.1066	0.2223	-0.0383	0.5999	-63.4779	16.9035	-47.3197
22	1.7992	-1.4843	-0.3709	4.7881	0.3086	5.7623	0.0551	0.1218	-0.1493	-0.2361	-0.2527	0.4303	0.2622	-0.0481	0.2014	0.2583	-0.0101	-0.0352	0.2148	-0.0333	0.2144	-51.3184	9.3722	-45.0185
23	3.5035	0.8966	1.0794	6.6939	0.5666	1.5642	0.174	-0.1027	-0.0513	-0.1996	-0.181	0.5677	0.105	-0.1824	-0.01	0.2693	0.001	-0.059	0.2845	0.0073	0.3379	-57.603	28.8869	-48.0069

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -4 through 3627 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 3628 through 3703 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 3704 through 3739 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 3740 through 3830 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 3831 through 3854 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 3855 through 3933 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 3934 through 3980 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 3981 through 4013 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 4014 through 4068 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid -4 through 3703 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 3704 through 3854 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 3855 through 4066 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid -4 through 3669 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 3670 through 3854 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 3855 through 4065 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid -4 through 3627 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 3628 through 3703 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 3704 through 3739 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 3740 through 3830 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 3831 through 3900 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 3901 through 3933 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 3934 through 3973 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 3974 through 4065 )

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