PDB-5kev: Vibrio parahaemolyticus VtrA/VtrC complex

ID or keywords:

Entry

Database: PDB / ID: 5kev

Title

Vibrio parahaemolyticus VtrA/VtrC complex

Components

VtrA Protein
VtrC Protein

Keywords

SIGNALING PROTEIN / heterodimer / alpha/beta / calycin beta barrel superfamily / bile salt receptor / TRANSCRIPTION

Function / homology

Function and homology information

phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / membrane / metal ion binding
Similarity search - Function

Biological species

Vibrio parahaemolyticus serotype O3:K6

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.7 Å

Model details

The C-terminal periplasmic domain of VtrA extends from residue 160 to 253. The C-terminal ...

Authors

Tomchick, D.R. / Orth, K. / Rivera-Cancel, G.

Citation

Journal: Elife / Year: 2016
Title: Bile salt receptor complex activates a pathogenic type III secretion system.
Authors: Li, P. / Rivera-Cancel, G. / Kinch, L.N. / Salomon, D. / Tomchick, D.R. / Grishin, N.V. / Orth, K.

History

Deposition	Jun 10, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5kev.cif.gz	141.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5kev_validation.pdf.gz	450.2 KB	Display	wwPDB validaton report
Full document	5kev_full_validation.pdf.gz	452.1 KB	Display
Data in XML	5kev_validation.xml.gz	9.5 KB	Display
Data in CIF	5kev_validation.cif.gz	11.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ke/5kev ftp://data.pdbj.org/pub/pdb/validation_reports/ke/5kev	HTTPS FTP

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Related structure data

Related structure data	5kewC C: citing same article (ref.)
Similar structure data	1gzf-2 4rva-d 6e5g-1 5b4d-2 1e6b-d 4k7a-d 2gbz-d 1qfj-4 3huh-1 2c8g-3 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
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (4)

Deposited unit

A: VtrA Protein

B: VtrC Protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

2

A: VtrA Protein

B: VtrC Protein

hetero molecules

A: VtrA Protein

B: VtrC Protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	211.012, 211.012, 211.012
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	209
Space group name H-M	F432

#1: Protein	VtrA Protein Mass: 10982.484 Da / Num. of mol.: 1 Fragment: VtrA C-terminal periplasmic domain, UNP residues 161-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria) Strain: RIMD 2210633 / Gene: VPA1332 / Plasmid: pACYCDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87GI4
#2: Protein	VtrC Protein Mass: 16918.775 Da / Num. of mol.: 1 Fragment: VtrC C-terminal periplasmic domain, UNP residues 31-161 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria) Strain: RIMD 2210633 / Gene: VPA1333 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87GI3
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 3.51 Å³/Da / Density % sol: 64.93 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 1.0 M lithium sulfate, 0.5 M ammonium sulfate, 0.1 M sodium citrate 28.7% ethylene glycol

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97935, 0.97927, 0.97943

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2015 / Details: monochromator

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97935	1
2	0.97927	1
3	0.97943	1

Reflection

Resolution: 2.65→40.609 Å / Num. obs: 12322 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 36.1 % / B_iso Wilson estimate: 37.51 Å² / CC_1/2: 0.934 / R_merge(I) obs: 0.076 / Net I/av σ(I): 63.565 / Net I/σ(I): 10.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.65-2.7	36.5	1.724	1	100
2.7-2.74	37.3	1.617	1	100
2.74-2.8	37.3	1.149	1	100
2.8-2.85	37.5	0.959	1	100
2.85-2.92	37.5	0.864	1	100
2.92-2.98	37.1	0.626	1	100
2.98-3.06	37.3	0.444	1	100
3.06-3.14	37.1	0.359	1	100
3.14-3.23	37.2	0.25	1	100
3.23-3.34	36.9	0.191	1	100
3.34-3.46	37.1	0.128	1	100
3.46-3.6	36.7	0.093	1	100
3.6-3.76	36.7	0.078	1	100
3.76-3.96	36.5	0.069	1	100
3.96-4.21	36.2	0.057	1	100
4.21-4.53	35.9	0.051	1	100
4.53-4.99	35.3	0.052	1	100
4.99-5.71	34.9	0.055	1	100
5.71-7.19	33.1	0.043	1	100
7.19-50	29.2	0.032	1	98.8

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Processing

Software

Name	Version	Classification
HKL-3000		data scaling
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.2	data extraction
HKL-3000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.7→40.609 Å / SU ML: 0.36 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.91

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2981	1470	12.68 %	random
R_work	0.26	-	-	-
obs	0.2649	11593	99.95 %	-

Solvent computation

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

Displacement parameters

B_iso max: 176.6 Å² / B_iso mean: 68.5081 Å² / B_iso min: 14.59 Å²

Refine analyze

Luzzati sigma a obs: 0.23 Å

Refinement step

Cycle: final / Resolution: 2.7→40.609 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1797	0	5	0	1802
B_iso mean	-	-	70.22	-	-
Num. residues	-	-	-	-	216

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	1841
X-RAY DIFFRACTION	f_angle_d	0.422	2490
X-RAY DIFFRACTION	f_chiral_restr	0.048	273
X-RAY DIFFRACTION	f_plane_restr	0.002	313
X-RAY DIFFRACTION	f_dihedral_angle_d	8.427	1091

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.7002-2.7873	0.3916	129	0.3399	899	1028	100
2.7873-2.8869	0.3343	129	0.3159	888	1017	100
2.8869-3.0025	0.3324	130	0.3155	895	1025	100
3.0025-3.1391	0.3376	131	0.2977	902	1033	100
3.1391-3.3045	0.3538	130	0.2974	898	1028	100
3.3045-3.5114	0.3076	130	0.2512	895	1025	100
3.5114-3.7824	0.2949	134	0.2524	916	1050	100
3.7824-4.1627	0.2655	134	0.2509	926	1060	100
4.1627-4.7642	0.2548	135	0.2052	924	1059	100
4.7642-5.9993	0.2802	137	0.2333	947	1084	100
5.9993-40.6139	0.2874	151	0.2613	1033	1184	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	0.0107	-0.011	0.0005	0.0331	-0.0289	0.0434	-0.0085	0.043	0.0628	-0.0013	0.009	0.0133	0.0474	0.0188	0.056	0.3433	-0.2381	0.2899	0.8416	0.2142	0.3725	227.6728	55.5542	18.4924
2	0.0173	-0.0127	-0.0079	0.01	-0.0058	0.0136	-0.0066	0.031	-0.0388	-0.0006	-0.0102	0.0004	0.0234	0.0735	0.0401	0.4136	-0.5411	0.4539	1.207	0.2122	0.1572	222.2624	56.9283	11.374
3	0.0694	0.0167	-0.0038	0.0314	0.0163	0.0121	-0.0227	0.002	-0.0076	-0.0129	-0.0163	0.0064	-0.0167	0.0037	-0.0263	0.463	-0.4028	-0.1458	0.6859	0.303	0.4957	217.6296	71.284	14.0683
4	0.0624	-0.0476	-0.05	0.0392	0.0345	0.0486	-0.1123	0.0365	-0.0588	0.0219	-0.0579	-0.0127	0.0055	0.1361	-0.1167	0.2293	-0.22	0.0893	0.6259	0.3029	0.0869	220.5907	54.1165	20.6176
5	0.0166	0.0029	-0.0007	0.0082	0.0143	0.0236	-0.074	0.0401	0.0212	0.0339	-0.0366	-0.0238	-0.0701	0.0184	-0.089	0.175	-0.6112	0.0135	0.5363	0.2798	0.1957	216.003	62.7126	23.5516
6	0.0019	0.0006	-0.0003	0.0003	-0.0001	0.0013	0.0219	0.0113	-0.0136	0.0101	0.0097	0.008	0.0103	-0.0065	-0	0.9292	-0.0778	0.0889	0.9384	-0.004	0.9104	210.8326	45.052	14.1712
7	0.0385	0.0022	-0.0595	0.0029	-0.0029	0.0951	-0.0417	-0.0052	0.0353	-0.0225	-0.0533	0.0205	-0.0193	0.0139	-0.1765	0.2741	-0.523	0.0266	0.5857	0.131	0.1442	210.846	59.655	13.6007
8	0.3276	0.1346	0.0122	0.1428	0.0229	0.0084	-0.0696	0.1064	0.025	0.0714	-0.0892	-0.1078	0.0137	-0.0655	-0.1501	0.2964	-0.5885	-0.1066	0.4044	0.1295	0.136	217.3477	61.6736	35.0143
9	0.0313	-0.0136	0.0027	0.0054	-0.0011	0.0004	-0.0215	-0.0334	0.0094	-0.0041	-0.0043	-0.0068	-0.0187	0.0082	-0.0052	0.334	-0.2269	-0.1489	0.6217	0.1144	0.284	202.2236	49.45	23.6226
10	0.0094	-0.01	0.0081	0.0943	-0.0493	0.1381	-0.0325	0.0581	0.0201	0.1567	-0.0672	-0.118	-0.0624	-0.049	-0.1323	-0.0471	-0.3165	-0.3931	0.2697	0.0493	-0.2742	211.5872	57.5856	37.7291
11	0.0075	0.0171	-0.0242	0.0982	-0.0703	0.0773	-0.0259	0.0232	0.0009	0.1143	-0.1118	-0.1347	-0.0476	0.0276	-0.2231	0.2558	-0.3253	0.0174	0.3976	0.19	0.0348	213.3596	53.9216	41.8195
12	0.0412	-0.02	0.054	0.0631	-0.022	0.0704	-0.0514	0.1243	0.0258	0.0573	-0.0563	-0.0854	-0.0355	0.1459	-0.084	0.0424	-0.3984	0.0578	0.3126	0.251	0.0276	223.2711	51.1407	41.3015
13	0.0071	0.006	0.0113	0.0067	0.009	0.0107	-0.0188	0.0131	0.0017	-0.0407	0.001	0.0272	0.0611	-0.0346	-0	0.4511	-0.1174	0.0865	0.5029	0.0201	0.5793	210.6021	45.1141	39.2897
14	0.0242	0.0216	-0.0094	0.0139	-0.007	0.0001	-0.0776	0.0289	0.0452	0.0156	-0.0217	-0.0876	-0.0329	0.186	-0.1631	-0.0977	-0.55	0.2468	0.5879	0.3259	0.0158	224.37	56.86	30.6796
15	0.0121	0.018	-0.0044	0.0176	-0.0058	0.0084	-0.0169	0.024	0.0466	0.0045	0.0058	-0.0113	-0.0129	0.0003	-0.0389	0.4589	-0.4151	0.0349	0.4892	0.1573	0.1581	221.6362	64.5828	33.4747

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 164 through 175 )	A	164 - 175
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 176 through 199 )	A	176 - 199
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 200 through 205 )	A	200 - 205
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 206 through 214 )	A	206 - 214
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 215 through 233 )	A	215 - 233
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 234 through 239 )	A	234 - 239
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 240 through 253 )	A	240 - 253
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 31 through 42 )	B	31 - 42
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 43 through 48 )	B	43 - 48
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 49 through 76 )	B	49 - 76
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 77 through 91 )	B	77 - 91
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 92 through 108 )	B	92 - 108
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 109 through 131 )	B	109 - 131
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 132 through 154 )	B	132 - 154
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 155 through 161 )	B	155 - 161

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