PDB-4jtm: Structure of the N0 domain of the type II secretin from enterotox...

ID or keywords:

Entry

Database: PDB / ID: 4jtm

Title

Structure of the N0 domain of the type II secretin from enterotoxigenic Escherichia coli

Components

Type II secretion system protein D

Keywords

PROTEIN TRANSPORT / general secretory pathway / secretin

Function / homology

Function and homology information

protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.43 Å

Authors

Korotkov, K.V. / Delarosa, J.R. / Hol, W.G.J.

Citation

Journal: J.Struct.Biol. / Year: 2013
Title: A dodecameric ring-like structure of the N0 domain of the type II secretin from enterotoxigenic Escherichia coli.
Authors: Korotkov, K.V. / Delarosa, J.R. / Hol, W.G.

History

Deposition	Mar 23, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 3, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2013	Group: Database references
Revision 1.2	Sep 11, 2013	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4jtm.cif.gz	81.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4jtm.ent.gz	64.1 KB	Display	PDB format
PDBx/mmJSON format	4jtm.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/jt/4jtm ftp://data.pdbj.org/pub/pdb/validation_reports/jt/4jtm	HTTPS FTP

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Related structure data

Related structure data	3ezj 3oss
Similar structure data	5v8t-2 4fn2-1 3o1f-d 3ci4-d 5j1n-d 2pwt-d 2h56-3 2h56-1 2fx0-d 1zzi-d 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	#211 - Jul 2017 Pilus Machine similarity (6)

Deposited unit

A: Type II secretion system protein D

B: Type II secretion system protein D

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

1

A: Type II secretion system protein D

B: Type II secretion system protein D

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

Unit cell

Length a, b, c (Å)	113.460, 113.460, 24.450
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

Details

BIOLOGICAL UNIT OF FULL-LENGTH GSPD IS A DODECAMER, THE HIGH-RESOLUTION DETAILS OF THIS ASSEMBLY ARE CURRENTLY UNAVAILABLE

#1: Protein	Type II secretion system protein D Mass: 8949.354 Da / Num. of mol.: 2 / Fragment: N0 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: H10407 / ETEC / Gene: ETEC_3237, GSPD / Plasmid: pRSF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3PJ86
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Type II secretion system protein D

Mass: 8949.354 Da / Num. of mol.: 2 / Fragment: N0 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: H10407 / ETEC / Gene: ETEC_3237, GSPD / Plasmid: pRSF-NT / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3PJ86

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.54 Å³/Da / Density % sol: 51.54 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M TRIS-HCL, 30% PEG2000-MME, pH 8.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 0.9795 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2011

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 1.43→49.18 Å / Num. obs: 59059 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 25.311 Å² / R_merge(I) obs: 0.044 / Net I/σ(I): 19.09

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
1.43-1.47		0.672	2.07	9245	2759	57.4
1.47-1.51		0.464	3.09	11221	3098	65.7
1.51-1.55		0.353	4.27	14107	3517	77.3
1.55-1.6		0.278	5.49	17718	4060	92
1.6-1.65		0.227	7.84	22493	4177	96.2
1.65-1.71		0.187	9.26	21657	3992	97.2
1.71-1.77		0.137	11.6	20612	3922	97.4
1.77-1.85		0.11	13.63	19129	3775	97.8
1.85-1.93		0.083	17.7	19707	3628	98
1.93-2.02		0.064	21.72	18812	3475	97.5
2.02-2.13		0.055	24.22	16912	3317	99.1
2.13-2.26		0.047	27.23	15608	3077	97.1
2.26-2.42		0.044	30.47	15820	2993	98.9
2.42-2.61		0.04	32.81	14161	2697	99
2.61-2.86		0.036	35.07	12394	2516	97.8
2.86-3.2		0.036	39.01	12087	2292	99
3.2-3.69		0.034	40.15	10393	2012	99.3
3.69-4.52		0.032	42.67	8411	1709	98.2
4.52-6.4		0.033	45.58	7054	1338	99.7
	6.4	0.03	45.59	3740	705	97.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
Blu-Ice		data collection
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.43→49.18 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.948 / WR_factor R_free: 0.2269 / WR_factor R_work: 0.1934 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8652 / SU B: 2.296 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0684 / SU R_free: 0.0726 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.073 / 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	0.2192	1612	5.1 %	RANDOM
R_work	0.1852	-	-	-
obs	0.1869	31494	92.74 %	-

Solvent computation

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

Displacement parameters

B_iso max: 59.69 Å² / B_iso mean: 22.4763 Å² / B_iso min: 9.87 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.16 Å²	-0.16 Å²	0 Å²
2-	-	-0.16 Å²	0 Å²
3-	-	-	0.53 Å²

Refinement step

Cycle: LAST / Resolution: 1.43→49.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1254	0	0	208	1462

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.02	1283
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1281
X-RAY DIFFRACTION	r_angle_refined_deg	1.694	1.98	1737
X-RAY DIFFRACTION	r_angle_other_deg	0.808	3	2947
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.88	5	164
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.69	25.769	52
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.9	15	237
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	26.478	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	206
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1448
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	276
X-RAY DIFFRACTION	r_mcbond_it	0.819	0.881	650
X-RAY DIFFRACTION	r_mcbond_other	0.812	0.878	649
X-RAY DIFFRACTION	r_mcangle_it	1.308	1.316	810

LS refinement shell

Resolution: 1.43→1.467 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.269	86	-
R_work	0.241	1439	-
all	-	1525	-
obs	-	-	61.57 %

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	15.709	-11.0703	4.7341	9.2031	0.0839	10.1376	-0.0948	0.2427	0.1301	0.0829	-0.0375	-0.1538	0.1776	0.3526	0.1323	0.1138	-0.0167	0.0873	0.1104	-0.0148	0.1857	60.952	-13.437	-2.418
2	19.407	-9.1947	11.3382	4.5918	-6.567	12.7388	-0.0845	0.1424	-0.316	0.0994	-0.098	0.0958	-0.3474	0.3087	0.1825	0.1238	-0.059	-0.0662	0.0886	0.0836	0.2045	48.987	-5.784	-10.076
3	4.8818	0.926	-5.4389	17.205	-8.38	9.2325	-0.1522	0.2478	0.1219	-0.3625	0.5094	0.5136	0.3141	-0.4881	-0.3572	0.1058	-0.0288	-0.0855	0.0969	0.0613	0.0973	38.258	-8.981	-10.033
4	11.3265	-6.7048	1.1747	14.1419	1.4228	6.9471	0.0984	0.6763	0.1702	-0.7895	0.0942	0.0796	-0.2131	-0.1756	-0.1926	0.1453	-0.0585	-0.0043	0.0953	0.0292	0.0458	42.471	-14.015	-8.242
5	5.8282	1.0973	2.0075	15.1714	-1.8546	5.6442	-0.0233	-0.2177	-0.2509	-0.1499	0.1095	-0.3138	-0.1027	-0.0879	-0.0861	0.0532	-0.0542	0.0327	0.0822	-0.0389	0.0832	49.605	-18.919	-5.574
6	22.1564	-1.0678	-2.864	5.9716	2.6891	3.9834	-0.0932	-0.026	0.3178	-0.1057	0.0167	0.1319	-0.1509	0.022	0.0765	0.0941	-0.0298	0.0044	0.056	0.0015	0.0815	41.097	-22.142	-3.263
7	13.0599	10.1349	-8.3145	34.8616	-18.3014	13.157	-0.0364	0.6949	0.7584	-0.3195	0.8317	1.6332	0.1082	-0.3666	-0.7953	0.0412	-0.0107	-0.051	0.1038	0.0095	0.1903	32.124	-11.708	-5.065
8	20.9381	-0.1134	7.4205	2.22	0.3837	2.7114	0.0042	-0.1473	-0.1484	-0.3743	-0.0003	0.2575	-0.0776	-0.0448	-0.004	0.1805	-0.0817	-0.0667	0.1334	0.0788	0.1797	48.892	-2.665	-6.444
9	7.662	2.1577	-1.6881	11.7434	-5.1516	3.8299	0.0825	-0.0411	0.1093	-0.0636	0.1481	0.0864	-0.0714	-0.0295	-0.2306	0.0609	-0.001	-0.0006	0.0665	-0.0045	0.0864	56.578	-10.464	0.88
10	4.9451	0.4381	2.9209	5.5135	3.1554	3.2591	-0.0927	-0.0056	-0.0859	0.0497	0.0792	0.0871	-0.0282	0.035	0.0135	0.083	-0.0138	-0.0007	0.0761	0.023	0.0948	50.821	-11.966	2.363
11	15.0774	-1.0726	-1.0872	4.9971	1.058	1.5621	-0.0865	-0.0546	0.0116	0.0595	-0.0255	0.1154	-0.0443	-0.0006	0.1119	0.0738	-0.0116	-0.0096	0.0462	0.0075	0.0836	43.503	-9.221	2.524
12	10.9956	5.6281	3.8605	9.9016	4.8375	4.914	-0.099	0.2836	0.2005	-0.2583	-0.1462	1.1609	-0.0801	0.0297	0.2452	0.0447	0.0059	-0.0175	0.074	-0.0556	0.2413	36.973	-10.485	2.61
13	4.1601	-1.0758	1.7296	4.5832	1.7507	3.3991	-0.2107	-0.315	-0.1531	0.3944	0.2324	-0.1722	0.0999	0.0556	-0.0217	0.129	0.0226	-0.0031	0.0867	0.0087	0.1036	43.597	-26.484	3.241
14	5.6438	0.4535	-1.7216	11.8352	1.4896	2.3782	0.0592	-0.2209	0.3125	0.2703	-0.0147	0.7868	0.023	-0.0644	-0.0445	0.0647	-0.0097	0.0091	0.0637	-0.0096	0.0913	37.027	-18.293	2.527
15	12.2995	-1.4001	5.0366	10.2135	-1.5816	10.9291	0.2223	0.2077	-0.8226	-0.0375	-0.0633	-0.4398	0.6752	0.5581	-0.159	0.0695	0.0219	0.0102	0.0366	-0.0204	0.1328	45.887	-40.718	-8.372
16	14.6154	-15.2609	1.2579	23.7135	-3.8859	1.147	0.5121	0.6779	-0.2842	-0.3678	-0.573	0.3926	-0.1604	-0.041	0.0609	0.183	0.0528	-0.0693	0.0957	-0.0381	0.1121	37.399	-26.899	-13.466
17	13.0874	8.7232	-5.5727	16.0653	-5.6794	5.5635	0.0455	0.2178	0.2453	0.0248	0.1841	0.8047	-0.147	-0.3965	-0.2296	0.0866	0.029	-0.0038	0.0641	0.0213	0.1516	26.799	-25.891	-11.792
18	9.7459	-3.9717	1.0057	7.6763	-1.2501	6.5049	0.0251	0.1694	0.2113	-0.2129	0.0423	0.1211	-0.2706	-0.1633	-0.0675	0.0222	0.0024	0.0018	0.0212	0.0255	0.1794	28.459	-32.866	-10.516
19	4.7464	2.568	1.5807	24.2331	-7.1731	10.9262	-0.1671	-0.3391	0.1093	0.1307	0.1215	0.3424	0.0226	-0.1372	0.0455	0.0135	0.0137	0.014	0.0619	-0.0001	0.0946	32.854	-40.162	-8.627
20	18.1917	-16.6189	-4.1028	15.4599	4.9674	6.5494	-0.4459	-0.3254	0.2954	0.3263	0.2977	-0.2156	-0.0568	0.003	0.1481	0.1532	-0.0665	0.0154	0.1507	0.0279	0.2297	24.141	-39.149	-5.009
21	15.1794	13.4879	-6.7826	14.103	-7.8124	4.805	0.2374	0.1103	1.5672	0.3272	0.4115	1.5126	-0.3319	-0.3729	-0.6488	0.1154	0.0515	0.0198	0.1048	0.0089	0.3386	22.151	-25.374	-7.085
22	23.9451	-11.2496	2.352	7.7432	-1.9839	1.4185	0.1951	-0.5416	0.9416	-0.3386	-0.0389	-0.4586	-0.2272	0.0822	-0.1561	0.1825	-0.0087	0.0824	0.0787	-0.0163	0.1359	40.854	-24.998	-9.71
23	9.4604	-0.884	-3.3925	8.2365	-2.9738	7.628	-0.2237	-0.075	-0.1151	0.227	0.1956	-0.405	-0.0076	0.1649	0.0281	0.0755	0.0087	-0.0093	0.0654	-0.0169	0.0912	43.945	-36.663	-4.658
24	5.0848	0.3938	0.3	4.5873	1.5931	3.6132	0.0088	-0.0851	-0.3148	0.1999	0.0557	0.1216	0.0555	0.0604	-0.0645	0.0877	-0.0033	0.0032	0.0578	0.0168	0.0742	38.787	-35.861	-2.193
25	7.9685	-0.5734	-0.6856	14.9172	1.6931	2.0939	0.0594	0.1989	0.0269	0.0005	-0.1219	0.5663	0.0602	-0.0729	0.0626	0.0661	-0.0065	0.0184	0.0413	0.0092	0.0733	34.632	-30.526	-1.195
26	21.4198	-5.5658	10.9722	16.3917	5.2892	12.096	-0.0543	-0.2309	0.3233	0.0875	-0.4116	0.8091	0.0968	-0.6046	0.4658	0.0666	-0.0361	0.0522	0.0623	-0.017	0.1968	28.319	-25.875	0.247
27	2.7526	0.9268	1.24	8.9211	2.5552	7.3297	-0.014	-0.1912	0.0388	0.4502	-0.1731	0.0348	0.013	0.03	0.1871	0.0435	-0.0077	-0.0013	0.122	0.0441	0.0932	24.695	-39.448	3.303
28	4.9101	0.7187	-0.1875	15.0263	0.6887	1.5899	0.1316	-0.2715	0.3835	0.1378	-0.1182	-0.0013	-0.0845	0.0135	-0.0135	0.0576	-0.0352	0.0021	0.1188	0.0162	0.0941	23.539	-36.578	0.196

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 5
2	X-RAY DIFFRACTION	2	A	6 - 10
3	X-RAY DIFFRACTION	3	A	11 - 15
4	X-RAY DIFFRACTION	4	A	16 - 20
5	X-RAY DIFFRACTION	5	A	21 - 26
6	X-RAY DIFFRACTION	6	A	27 - 31
7	X-RAY DIFFRACTION	7	A	32 - 38
8	X-RAY DIFFRACTION	8	A	39 - 44
9	X-RAY DIFFRACTION	9	A	45 - 50
10	X-RAY DIFFRACTION	10	A	51 - 54
11	X-RAY DIFFRACTION	11	A	55 - 61
12	X-RAY DIFFRACTION	12	A	62 - 67
13	X-RAY DIFFRACTION	13	A	68 - 73
14	X-RAY DIFFRACTION	14	A	74 - 80
15	X-RAY DIFFRACTION	15	B	0 - 5
16	X-RAY DIFFRACTION	16	B	6 - 10
17	X-RAY DIFFRACTION	17	B	11 - 15
18	X-RAY DIFFRACTION	18	B	16 - 20
19	X-RAY DIFFRACTION	19	B	21 - 26
20	X-RAY DIFFRACTION	20	B	27 - 31
21	X-RAY DIFFRACTION	21	B	32 - 39
22	X-RAY DIFFRACTION	22	B	40 - 44
23	X-RAY DIFFRACTION	23	B	45 - 50
24	X-RAY DIFFRACTION	24	B	51 - 54
25	X-RAY DIFFRACTION	25	B	55 - 59
26	X-RAY DIFFRACTION	26	B	60 - 65
27	X-RAY DIFFRACTION	27	B	66 - 71
28	X-RAY DIFFRACTION	28	B	72 - 80

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Yorodumi