PDB-4ftf: Structure of the Type II secretion system pilotin AspS from Vibri...

ID or keywords:

Entry

Database: PDB / ID: 4ftf

Title

Structure of the Type II secretion system pilotin AspS from Vibrio cholerae

Components

Alternate secretin pathway subunit S (VC395_1821, VC1703)

Keywords

PROTEIN TRANSPORT / pilotin /

lipoprotein /

secretin /

protein secretion / PfamB PB000779 /

secretin binding / outer membrane

Function / homology

GMP Synthetase; Chain A, domain 3 - #250 /

Type II secretion system (T2SS) pilotin, S protein /

GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich /

metal ion binding / Alpha Beta /

ACETATE ION / Uncharacterized protein

Function and homology information

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.48 Å

Authors

Korotkov, K.V. / Evans, T.J.

Citation

Journal: Plos Pathog. / Year: 2013
Title: Assembly of the Type II Secretion System such as Found in Vibrio cholerae Depends on the Novel Pilotin AspS.
Authors: Dunstan, R.A. / Heinz, E. / Wijeyewickrema, L.C. / Pike, R.N. / Purcell, A.W. / Evans, T.J. / Praszkier, J. / Robins-Browne, R.M. / Strugnell, R.A. / Korotkov, K.V. / Lithgow, T.

History

Deposition	Jun 27, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 28, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 6, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ftf.cif.gz	58.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4ftf.ent.gz	46.7 KB	Display	PDB format
PDBx/mmJSON format	4ftf.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/ft/4ftf ftp://data.pdbj.org/pub/pdb/validation_reports/ft/4ftf	HTTPS FTP

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Related structure data

Similar structure data	2o6p-1 4ezf-d 5zqh-d 6fuu-d 4lup-2 1j6y-d 1lxg-d 2ezi-d 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: Alternate secretin pathway subunit S (VC395_1821, VC1703)

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	34.160, 63.860, 47.540
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Alternate secretin pathway subunit S (VC395_1821, VC1703) Mass: 12259.997 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 55-163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: 569B / Gene: VC395_1821, VC_1703 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9KRD9
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.11 Å³/Da / Density % sol: 41.84 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M ZINC ACETATE, 20% PEG 3350, pH 7.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2012

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.48→47.54 Å / Num. all: 17954 / Num. obs: 17689 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 20.123 Å² / R_merge(I) obs: 0.084 / Net I/σ(I): 16.17

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.48-1.52		0.958	1.43	9662	2074	84.8
1.52-1.56		0.743	2.03	12066	2256	93.3
1.56-1.61		0.589	2.99	15382	2345	99.1
1.61-1.65		0.529	3.7	17051	2253	100
1.65-1.71		0.411	4.82	17051	2241	100
1.71-1.77		0.327	6.03	16437	2155	100
1.77-1.84		0.242	8.19	15650	2052	100
1.84-1.91		0.185	10.8	15181	1988	100
1.91-2		0.143	13.81	14568	1898	100
2-2.09		0.118	16.91	13963	1819	100
2.09-2.21		0.089	21.25	13121	1705	100
2.21-2.34		0.077	23.81	12961	1679	100
2.34-2.5		0.066	26.78	11778	1527	100
2.5-2.7		0.06	28.86	10991	1424	100
2.7-2.96		0.053	33.85	10190	1321	100
2.96-3.31		0.042	39.32	9045	1186	100
3.31-3.82		0.036	44.82	7972	1053	100
3.82-4.68		0.033	48.97	6690	885	100
4.68-6.62		0.033	46.41	5300	698	100
	6.62	0.03	48.96	2729	371	100

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
SHARP		phasing
SOLOMON		phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
SERGUI		data collection
XDS		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 1.48→47.54 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.957 / WR_factor R_free: 0.1765 / WR_factor R_work: 0.155 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9095 / SU B: 1.996 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0671 / SU R_free: 0.0664 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1765	907	5.1 %	RANDOM
R_work	0.155	-	-	-
all	0.1561	17954	-	-
obs	0.1561	17689	98.5 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 50.64 Å² / B_iso mean: 17.1693 Å² / B_iso min: 7.28 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.4 Å²	0 Å²	0 Å²
2-	-	0.59 Å²	0 Å²
3-	-	-	-0.19 Å²

Refinement step

Cycle: LAST / Resolution: 1.48→47.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	830	0	15	169	1014

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	870
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	592
X-RAY DIFFRACTION	r_angle_refined_deg	1.529	1.992	1174
X-RAY DIFFRACTION	r_angle_other_deg	0.883	3.003	1457
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.216	5	116
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.2	25.263	38
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.629	15	169
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.35	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	138
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	972
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	155

LS refinement shell

Resolution: 1.48→1.519 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.248	37	-
R_work	0.232	982	-
all	-	1019	-
obs	-	-	84.92 %

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	12.3079	-2.4675	0.755	7.4135	0.509	5.3306	0.1636	0.4466	-0.3782	0.0256	-0.1427	-0.0265	0.1025	0.1977	-0.0209	0.0364	-0.0033	-0.0092	0.111	-0.0237	0.0154	34.516	13.69	12.879
2	2.8422	-0.9352	-0.4706	3.6028	2.7382	7.4785	-0.0033	0.0182	-0.0795	0.046	-0.02	0.0564	0.0633	0.1198	0.0232	0.0263	0.0008	-0.0004	0.0691	-0.0108	0.0178	30.511	17.976	19.699
3	1.8801	-1.2469	-2.3069	3.8197	3.9571	8.8922	-0.022	-0.1156	0.0129	0.0329	-0.1094	0.1062	-0.0463	-0.2107	0.1314	0.0265	0.0008	0.001	0.0701	-0.0162	0.0397	24.225	23.766	30.265
4	3.7791	-11.3105	6.1276	33.8833	-18.026	13.0452	-0.0308	-0.0717	-0.2404	0.1189	0.1865	0.7417	0.2211	-0.3409	-0.1558	0.0696	-0.0436	-0.003	0.1039	0.0227	0.0903	26.369	22.215	41.432
5	3.6687	-1.5863	1.1163	14.3227	-8.2848	11.6375	0.0516	-0.3791	-0.1839	0.4248	-0.0486	0.0756	-0.2547	0.0333	-0.0031	0.0212	-0.0102	-0.0061	0.0786	0.01	0.022	31.116	23.682	42.605
6	3.0375	-2.3417	-3.9117	3.4602	6.3445	11.7365	0.0772	0.0004	0.1144	-0.2414	0.107	-0.1103	-0.4743	0.2235	-0.1842	0.0785	-0.0194	-0.008	0.0502	0.0098	0.04	34.646	24.703	26.867
7	6.9094	-1.8459	-3.7774	5.3119	8.0639	20.084	0.1399	-0.3151	0.0401	-0.2396	-0.0003	-0.1748	-0.4346	0.282	-0.1396	0.0393	-0.0061	-0.0069	0.0485	0.0005	0.0367	34.987	24.571	34.086
8	2.0854	-0.1036	3.5088	2.1475	-5.7186	20.2859	-0.0367	-0.0681	0.0343	0.1754	0.0497	0.0294	-0.4732	-0.2714	-0.0129	0.0747	0.0021	0.0098	0.1001	-0.0108	0.0176	36.985	24.997	52.554
9	5.3394	0.627	2.1566	6.1252	0.6309	13.5987	-0.0479	-0.165	0.0544	0.0991	-0.1241	-0.2284	0.0675	-0.0114	0.1721	0.0538	0.0117	-0.0103	0.0728	0.0272	0.0231	41.976	17.113	48.316
10	16.6212	12.0068	7.7133	12.9936	5.3539	10.783	0.3141	-0.2824	-0.6211	0.3347	-0.1092	-0.5194	0.2436	0.0984	-0.205	0.0604	0.0166	-0.0066	0.0754	0.0253	0.0284	37.857	13.144	41.863
11	8.3373	-2.0211	3.9371	3.3579	2.6122	11.2377	0.1491	-0.3393	-0.4006	0.0817	0.0782	0.1041	-0.0313	-0.4294	-0.2273	0.0614	-0.0129	0.0204	0.067	0.0343	0.0604	29.788	10.167	36.638
12	4.4256	0.5993	-1.9811	1.9717	-1.54	6.1834	-0.0334	0.0334	-0.1488	-0.1058	-0.0025	0.0752	0.0705	-0.1822	0.0359	0.0424	-0.004	-0.0032	0.0381	-0.012	0.039	31.201	10.261	28.487
13	3.2398	3.1714	5.6567	6.1225	8.0683	12.0855	-0.0584	0.0708	-0.0666	-0.0778	0.1981	-0.0327	-0.0926	0.3137	-0.1397	0.0478	0.0197	-0.006	0.0992	-0.0287	0.0569	38.17	20.443	33.304
14	8.1289	-2.5575	-6.9737	19.0218	1.2249	7.6209	0.1784	-0.123	0.4548	0.3191	0.0654	-0.665	-0.4358	0.2751	-0.2438	0.0697	-0.0026	-0.0257	0.0959	-0.0087	0.0591	41.388	31.116	44.223
15	3.1658	1.5091	5.2461	13.8765	12.7984	16.754	0.0347	0.0423	-0.0192	-0.0203	0.1379	-0.1856	0.0316	0.1729	-0.1725	0.0259	-0.0034	0.0141	0.1041	-0.0056	0.0309	42.564	19.798	36.145
16	13.2914	0.9742	-4.2915	8.8633	-5.2118	21.071	-0.0754	0.0033	-0.8602	-0.0605	-0.0602	-0.1764	0.598	0.3184	0.1356	0.0517	0.0229	-0.0085	0.0321	0.0028	0.076	40.327	7.771	31.226

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 10
2	X-RAY DIFFRACTION	2	A	11 - 17
3	X-RAY DIFFRACTION	3	A	18 - 27
4	X-RAY DIFFRACTION	4	A	28 - 31
5	X-RAY DIFFRACTION	5	A	32 - 37
6	X-RAY DIFFRACTION	6	A	38 - 45
7	X-RAY DIFFRACTION	7	A	46 - 50
8	X-RAY DIFFRACTION	8	A	51 - 59
9	X-RAY DIFFRACTION	9	A	60 - 65
10	X-RAY DIFFRACTION	10	A	66 - 71
11	X-RAY DIFFRACTION	11	A	72 - 77
12	X-RAY DIFFRACTION	12	A	78 - 87
13	X-RAY DIFFRACTION	13	A	88 - 93
14	X-RAY DIFFRACTION	14	A	94 - 100
15	X-RAY DIFFRACTION	15	A	101 - 106
16	X-RAY DIFFRACTION	16	A	107 - 111

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