PDB-4dq9: Crystal structure of the minor pseudopilin EPSH from the type II ...

ID or keywords:

Entry

Database: PDB / ID: 4dq9

Title

Crystal structure of the minor pseudopilin EPSH from the type II secretion system of Vibrio cholerae

Components

General secretion pathway protein H

Keywords

TRANSPORT PROTEIN /

Type II secretion system / pseudopilin / pseudopilus

Function / homology

Function and homology information

protein secretion by the type II secretion system /

type II protein secretion system complex /

plasma membrane
Similarity search - Function

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.59 Å

Authors

Raghunathan, K. / Vago, F.S. / Grindem, D. / Ball, T. / Wedemeyer, W.J. / Arvidson, D.N.

Citation

Journal: Biochim.Biophys.Acta / Year: 2013
Title: The 1.59 angstrom resolution structure of the minor pseudopilin EpsH of Vibrio cholerae reveals a long flexible loop.
Authors: Raghunathan, K. / Vago, F.S. / Grindem, D. / Ball, T. / Wedemeyer, W.J. / Bagdasarian, M. / Arvidson, D.N.

History

Deposition	Feb 15, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 8, 2014	Group: Database references
Revision 1.2	Feb 28, 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4dq9.cif.gz	137.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4dq9.ent.gz	109.8 KB	Display	PDB format
PDBx/mmJSON format	4dq9.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/dq/4dq9 ftp://data.pdbj.org/pub/pdb/validation_reports/dq/4dq9	HTTPS FTP

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Related structure data

Related structure data	2qv8
Similar structure data	3cz6-3 5x11-3 2px9-d 2wc8-d 5aa3-2 1s7w-2 5e8o-1 3ch1-2 5aa1-1 5nqe-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (3)

Deposited unit

A: General secretion pathway protein H

B: General secretion pathway protein H

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

A: General secretion pathway protein H

hetero molecules

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

3

B: General secretion pathway protein H

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.391, 71.110, 84.646
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	General secretion pathway protein H / Cholera toxin secretion protein epsH Mass: 19545.613 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 33-194 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: epsH, VC_2729 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P45774
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.06 Å³/Da / Density % sol: 40.15 %
Crystal grow	pH: 7.5 Details: 7% PEG 4000, 90MM sodium acetate, 10MM Tris-HCl, 175MM sodium formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 1.59→27.94 Å / Num. obs: 43721 / % possible obs: 85.9 % / Observed criterion σ(I): 1

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.59→27.94 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.94 / SU B: 4.947 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.249	2128	5.1 %	RANDOM
R_work	0.201	-	-	-
obs	0.204	39974	96.3 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 27.58 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.12 Å²	0 Å²	0 Å²
2-	-	-0.21 Å²	0 Å²
3-	-	-	0.1 Å²

Refinement step

Cycle: LAST / Resolution: 1.59→27.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2300	0	3	254	2557

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.025	0.022	2408
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1650
X-RAY DIFFRACTION	r_angle_refined_deg	2.095	1.96	3261
X-RAY DIFFRACTION	r_angle_other_deg	1.106	3	4024
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.511	5	298
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.862	25.44	125
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.717	15	419
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.62	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.136	0.2	354
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	2707
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	476
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.307	1.5	1477
X-RAY DIFFRACTION	r_mcbond_other	0.406	1.5	605
X-RAY DIFFRACTION	r_mcangle_it	2.054	2	2364
X-RAY DIFFRACTION	r_scbond_it	3.259	3	931
X-RAY DIFFRACTION	r_scangle_it	5.023	4.5	895
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.59→1.64 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.422	105	-
R_work	0.411	2229	-
obs	-	-	73.26 %

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	3.2447	-0.1293	-0.3555	1.6538	0.6646	2.4488	-0.0195	0.149	0.2347	-0.0054	0.1066	0.0515	-0.2582	-0.0611	-0.0872	0.1337	0.0066	0.0001	0.1138	-0.0016	0.1165	29.9528	58.9997	5.9055
2	1.9015	0.2233	0.0313	2.9089	-0.8515	2.917	0.0223	-0.1198	-0.1115	0.2571	0.0075	0.1649	0.0337	-0.1655	-0.0297	0.1045	-0.0017	0.0281	0.1117	0.0065	0.1037	24.2584	42.1717	15.3379
3	6.6563	4.3134	-5.2373	3.7092	-2.6416	4.7516	-0.2275	0.058	-0.1374	-0.0887	0.0609	-0.0525	0.2657	-0.0139	0.1666	0.1272	0.0222	0.0074	0.1367	0.0191	0.1341	34.0108	41.3937	6.5069
4	9.9001	-0.8889	-3.6156	3.436	-1.5996	7.7017	-0.1102	0.4006	-0.1256	-0.3752	0.0384	-0.0405	0.1327	-0.1197	0.0718	0.1214	-0.0115	-0.0054	0.1216	0.0024	0.0965	36.3602	47.8791	-2.2111
5	2.0941	-2.1981	0.6496	13.9469	-4.1336	2.0067	0.1015	0.0235	-0.2326	-0.2336	0.0411	0.6786	0.2843	-0.008	-0.1425	0.1251	-0.0054	-0.0329	0.1031	-0.0165	0.1076	28.2642	33.2507	6.6646
6	0.7277	0.1958	0.629	1.0757	-0.4027	0.9104	0.044	0.0219	0.0103	-0.149	0.0023	0.1441	0.1007	-0.0414	-0.0463	0.0901	0.0073	-0.007	0.1231	-0.0108	0.1168	25.1631	41.633	3.6438
7	1.1997	1.1538	-1.5175	3.803	-1.6105	1.9898	0.0183	0.0019	0.079	-0.146	-0.0127	-0.1302	-0.0015	0.057	-0.0056	0.1279	0.0046	0.0091	0.1569	0.0024	0.1514	40.4726	52.2959	4.6679
8	2.3708	-0.5077	-3.3965	0.4448	1.4367	6.3728	-0.1403	-0.0637	-0.0671	-0.0017	0.0181	0.0097	0.134	0.0836	0.1222	0.0846	-0.0012	-0.0132	0.1085	0.0261	0.1432	48.1772	50.3985	2.3679
9	0.651	-0.2694	-0.2622	4.7912	3.3176	2.3067	-0.08	0.4455	0.0902	0.2337	-0.3427	0.607	0.179	-0.3025	0.4227	0.135	-0.1085	-0.0286	0.3218	0.0503	0.1394	43.365	46.7599	-10.8597
10	0.0083	0.1268	0.4561	2.2037	7.9074	28.3804	-0.0998	-0.007	0.0197	0.0109	-0.4888	0.1814	0.0634	-1.3687	0.5886	0.1507	0.0324	0.1139	0.3979	0.1288	0.296	37.6198	35.3644	-9.8928
11	2.669	0.2552	0.1681	2.0788	-0.4694	0.5931	0.0241	-0.1718	-0.1138	0.1356	-0.0505	0.0732	0.0549	-0.0033	0.0263	0.1181	0.0006	-0.0101	0.1157	0.0138	0.0937	35.5381	40.9982	14.1246
12	3.6731	1.5955	-0.7394	3.3494	-2.6003	4.4143	-0.031	0.125	0.0774	-0.0585	-0.0588	-0.2311	-0.0611	0.1459	0.0898	0.1211	-0.0026	0.0077	0.0997	0.001	0.1185	41.0059	58.7288	2.6872
13	1.5605	0.8344	-0.3725	2.5455	-1.9132	1.9453	-0.0177	-0.3013	0.0298	0.4463	-0.1498	-0.2428	-0.1921	0.1626	0.1675	0.1953	0.0221	-0.0391	0.1091	-0.0234	0.0911	38.7239	53.4282	16.0372
14	0.9366	1.6885	-3.4882	10.5676	-9.4186	14.4824	0.0202	-0.197	-0.0568	0.7631	-0.1922	-0.0383	-0.4329	0.463	0.1719	0.1851	0.0179	-0.0014	0.2565	0.0111	0.0724	34.3843	55.4796	18.2294
15	2.2474	-2.0984	-5.0254	4.4057	5.2609	11.3799	-0.4534	-0.2204	-0.152	0.4423	0.3175	-0.5045	1.0356	0.5231	0.1359	0.163	0.0605	-0.0816	0.0314	-0.0281	0.4208	44.9486	-0.4199	13.506
16	2.3531	-1.2432	-1.0749	2.0391	1.3936	2.138	-0.0272	-0.1068	-0.1504	0.0686	0.0251	0.12	0.0383	-0.0019	0.0021	0.1091	0.0068	0.018	0.1075	0.0152	0.1252	34.8512	16.6021	21.167
17	8.4197	-4.7729	-8.3498	6.2608	5.6537	10.5771	0.2665	0.1353	0.0703	-0.306	-0.1169	-0.2236	-0.228	0.1148	-0.1496	0.1301	0.006	-0.0006	0.1466	0.0079	0.1037	40.313	22.1527	12.13
18	6.0019	0.0707	6.8213	1.2496	-3.9309	20.6439	-0.1911	0.6899	-0.0981	-0.1032	-0.1208	-0.149	0.1057	1.142	0.3118	0.0741	-0.0089	0.1323	0.1881	-0.0057	0.2475	49.8051	16.344	7.7391
19	1.9539	-4.9559	-0.2015	19.3193	0.9682	1.8526	-0.1229	-0.0369	0.2012	0.3483	0.0737	-0.4724	-0.1655	0.0759	0.0492	0.1017	-0.0129	-0.03	0.1126	0.0067	0.1259	41.2165	29.0039	17.212
20	2.587	-0.3502	0.1767	0.6501	0.5431	0.5668	-0.1419	-0.2321	-0.0633	0.0506	0.1339	-0.0278	0.0062	0.1252	0.0081	0.1121	-0.0022	-0.0096	0.1574	0.0661	0.154	44.1846	21.9265	20.5919
21	0.8819	-0.0894	-1.1871	4.5265	2.1275	2.498	-0.1203	0.1215	-0.1394	-0.3954	-0.006	-0.1167	-0.0098	-0.1154	0.1262	0.1597	0.0279	0.032	0.2621	-0.0344	0.1119	41.8383	11.2158	5.5863
22	23.2993	21.4162	5.6224	19.9944	5.3104	1.4229	0.1266	-0.1424	0.1932	0.0927	-0.1351	0.1063	0.0197	-0.0246	0.0085	0.2745	-0.1607	-0.1567	0.2664	0.1328	0.1264	50.3805	26.2033	4.9244
23	0.2371	0.4542	0.2126	0.9553	0.4509	0.2174	-0.0574	0.1151	0.0199	0.086	0.0787	0.0887	0.0567	0.0482	-0.0214	0.2223	-0.1417	0.0207	0.204	-0.0197	0.2007	58.4373	39.7991	15.4681
24	0.9741	-0.7458	0.9001	3.1617	-0.1732	2.8542	-0.0202	0.0072	-0.1138	-0.0115	-0.054	0.3399	-0.1268	-0.1884	0.0742	0.1193	0.0058	-0.011	0.1	-0.0162	0.1291	31.7101	22.903	12.0482
25	4.7839	-4.5237	-2.211	7.2307	2.8281	2.6811	0.1055	0.1631	-0.2093	-0.2883	-0.0242	-0.1241	-0.0237	0.2363	-0.0813	0.1064	0.0087	0.0174	0.1106	-0.0445	0.1474	42.4339	5.9302	5.6544
26	2.8348	-1.6743	-0.8564	5.7398	0.896	4.5037	0.0386	0.3268	-0.0852	-0.2876	-0.0348	0.3981	0.0251	-0.2987	-0.0038	0.1264	-0.0199	-0.0252	0.1173	-0.0202	0.1835	33.8704	6.6149	6.9179
27	13.0529	-13.8637	-0.9614	43.1435	-6.2167	8.0676	-0.6076	0.1206	-0.1362	1.4235	0.9812	2.1138	-0.7136	-1.6188	-0.3736	0.1154	0.1382	0.1115	0.3343	0.0197	0.3964	26.4445	11.2982	14.5766
28	28.4808	-4.5139	-3.7023	3.7469	0.8412	0.505	-0.694	1.6732	-0.6946	0.0912	0.5861	0.1824	0.0861	-0.1671	0.1079	0.0354	-0.0299	-0.0008	0.5502	-0.2432	0.2603	29.7449	0.3532	8.4003

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	27 - 41
2	X-RAY DIFFRACTION	2	A	42 - 55
3	X-RAY DIFFRACTION	3	A	56 - 63
4	X-RAY DIFFRACTION	4	A	64 - 68
5	X-RAY DIFFRACTION	5	A	69 - 78
6	X-RAY DIFFRACTION	6	A	79 - 93
7	X-RAY DIFFRACTION	7	A	94 - 106
8	X-RAY DIFFRACTION	8	A	107 - 113
9	X-RAY DIFFRACTION	9	A	114 - 122
10	X-RAY DIFFRACTION	10	A	123 - 136
11	X-RAY DIFFRACTION	11	A	137 - 153
12	X-RAY DIFFRACTION	12	A	154 - 162
13	X-RAY DIFFRACTION	13	A	163 - 174
14	X-RAY DIFFRACTION	14	A	175 - 183
15	X-RAY DIFFRACTION	15	B	27 - 33
16	X-RAY DIFFRACTION	16	B	34 - 55
17	X-RAY DIFFRACTION	17	B	56 - 63
18	X-RAY DIFFRACTION	18	B	64 - 67
19	X-RAY DIFFRACTION	19	B	68 - 78
20	X-RAY DIFFRACTION	20	B	79 - 93
21	X-RAY DIFFRACTION	21	B	94 - 106
22	X-RAY DIFFRACTION	22	B	107 - 124
23	X-RAY DIFFRACTION	23	B	125 - 137
24	X-RAY DIFFRACTION	24	B	138 - 152
25	X-RAY DIFFRACTION	25	B	153 - 161
26	X-RAY DIFFRACTION	26	B	162 - 173
27	X-RAY DIFFRACTION	27	B	174 - 179
28	X-RAY DIFFRACTION	28	B	180 - 186

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The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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