PDB-2vmb: The three-dimensional structure of the cytoplasmic domains of Eps...

ID or keywords:

Entry

Database: PDB / ID: 2vmb

Title

The three-dimensional structure of the cytoplasmic domains of EpsF from the Type 2 Secretion System of Vibrio cholerae

Components

GENERAL SECRETION PATHWAY PROTEIN F

Keywords

TRANSPORT PROTEIN /

TRANSMEMBRANE / INNER MEMBRANE / TYPE 2 SECRETION / T4PB /

T2SS /

VIBRIO /

CHOLERA /

MEMBRANE / TRANSPORT /

PROTEIN SECRETION

Function / homology

Function and homology information

protein secretion by the type II secretion system /

type II protein secretion system complex /

metal ion binding /

plasma membrane
Similarity search - Function

Biological species

VIBRIO CHOLERAE (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.95 Å

Authors

Abendroth, J. / Korotkov, K.V. / Mitchell, D.D. / Kreger, A. / Hol, W.G.J.

Citation

Journal: J.Struct.Biol. / Year: 2009
Title: The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf from the Type 2 Secretion System of Vibrio Cholerae.
Authors: Abendroth, J. / Mitchell, D.D. / Korotkov, K.V. / Johnson, T.L. / Kreger, A. / Sandkvist, M. / Hol, W.G.

History

Deposition	Jan 25, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 10, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jun 28, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	May 8, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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	2vmb.cif.gz	65.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2vmb.ent.gz	50.7 KB	Display	PDB format
PDBx/mmJSON format	2vmb.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/vm/2vmb ftp://data.pdbj.org/pub/pdb/validation_reports/vm/2vmb	HTTPS FTP

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Related structure data

Related structure data	2vmaC 3c1qC C: citing same article (ref.)
Similar structure data	2vma-1 2a4j-d 2mfq-d 2dlu-d 2da0-d 1m7e-1 6fgp-d 2jkf-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 (4)

Deposited unit

A: GENERAL SECRETION PATHWAY PROTEIN F

B: GENERAL SECRETION PATHWAY PROTEIN F

hetero molecules

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

1

A: GENERAL SECRETION PATHWAY PROTEIN F

hetero molecules

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

2

B: GENERAL SECRETION PATHWAY PROTEIN F

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.197, 53.832, 89.070
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	6	A	1 - 122
2	1	1	6	B	1 - 122

NCS oper: (Code: given
Matrix: (-0.99981, -0.00695, -0.01803), (0.01676, 0.15209, -0.98823), (0.00961, -0.98834, -0.15194)
Vector: 40.14479, 77.84767, 91.40726)

#1: Protein	GENERAL SECRETION PATHWAY PROTEIN F / CHOLERA TOXIN SECRETION PROTEIN EPSF / EPSF Mass: 13843.822 Da / Num. of mol.: 2 / Fragment: RESIDUES 56-170 Source method: isolated from a genetically manipulated source Details: RESIDUES 56-170, PLUS C-TERMINAL TEV- CLEAVABLE HIS6-TAG Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Plasmid: PACYC-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): N / References: UniProt: P45780
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	CYTOPLASMIC DOMAIN, RESIDUES 56-171, PLUS C-TERMINAL TEV CLEAVAGE SITE

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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 Å³/Da / Density % sol: 38.08 % / Description: NONE
Crystal grow	pH: 7 Details: 1UL PROTEIN, 1UL RESERVOIR: 12.5% PEG 400, 200MM CAOAC2, 100MM MES PH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 2.0663
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jan 29, 2007 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 2.0663 Å / Relative weight: 1
Reflection	Resolution: 1.95→46.07 Å / Num. obs: 16364 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 12.96 % / R_merge(I) obs: 0.05 / Net I/σ(I): 36
Reflection shell	Resolution: 1.95→2.02 Å / Redundancy: 8.43 % / R_merge(I) obs: 0.14 / Mean I/σ(I) obs: 10.2 / % possible all: 59.1

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Processing

Software

Name	Version	Classification
ARP/wARP		model building
CrystalClear		data scaling
SHELX		phasing
SHARP		phasing
DM		phasing
ARP/wARP		phasing
REFMAC	5.2.0019	refinement

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.95→46.08 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.911 / SU B: 7.203 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.251	834	5.1 %	RANDOM
R_work	0.189	-	-	-
obs	0.192	15530	91.7 %	-

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 mean: 25.89 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.22 Å²	0 Å²	0 Å²
2-	-	0.87 Å²	0 Å²
3-	-	-	-1.09 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→46.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1851	0	2	207	2060

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1921
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1344
X-RAY DIFFRACTION	r_angle_refined_deg	1.13	1.985	2596
X-RAY DIFFRACTION	r_angle_other_deg	0.975	3	3275
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.121	5	248
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.888	23.556	90
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.82	15	361
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.157	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	294
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2145
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	390
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	457
X-RAY DIFFRACTION	r_nbd_other	0.183	0.2	1333
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	965
X-RAY DIFFRACTION	r_nbtor_other	0.079	0.2	961
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	150
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	0.246	0.2	24
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.234	0.2	71
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.294	0.2	23
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	0.558	1.5	1271
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.769	2	1925
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.542	3	758
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.249	4.5	665
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 738 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
loose positional	0.43	5
loose thermal	0.77	10

LS refinement shell

Resolution: 1.95→2 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.411	42	-
R_work	0.334	683	-
obs	-	-	55.98 %

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	0.9278	-1.972	-3.1448	11.3604	19.0675	32.0496	0.2151	0.4354	-0.2259	-0.636	-0.3471	0.0618	-0.7565	-0.2837	0.132	-0.0339	-0.007	-0.0008	-0.0015	-0.0112	-0.1168	23.416	24.277	31.4312
2	3.06	-1.5359	1.6595	5.3596	-4.5713	10.1605	-0.0104	-0.2591	0.0122	0.072	0.1862	0.0268	0.2167	0.1323	-0.1759	-0.181	0.0165	0.0072	-0.1139	-0.0346	-0.1792	23.4469	24.8055	54.1484
3	32.4331	-11.2155	12.4038	11.4051	2.3548	23.0602	0.5094	-0.4906	-1.6085	0.6873	-0.0683	0.4163	1.2931	-0.2904	-0.4411	-0.0483	-0.0102	-0.007	-0.1546	0.0726	-0.1321	21.0957	14.6645	54.0577
4	7.0758	-1.6054	4.3943	1.1324	2.5904	19.4826	-0.145	0.3013	-0.087	0.1908	-0.0417	0.0571	-0.3629	-0.5264	0.1867	-0.145	-0.0144	-0.0167	-0.1208	-0.0223	-0.1643	13.6606	22.1192	46.5846
5	15.1395	-5.5373	10.9501	22.9937	-9.6858	10.0577	-0.4212	0.3212	0.2359	-0.1577	0.1085	0.8255	-0.1934	0.0671	0.3127	-0.0853	-0.058	0.0022	-0.107	-0.0458	-0.1681	17.4078	18.9207	41.5429
6	20.5973	-1.0282	13.4468	10.1066	-2.9317	9.2867	-0.1267	0.4753	-0.91	-0.1821	-0.0517	-0.7553	0.9355	0.3882	0.1784	0.0037	0.0465	0.0753	-0.1561	-0.0154	-0.0472	25.8223	9.4149	47.2035
7	27.3614	-1.4747	16.2625	2.7317	-2.3893	10.5286	-0.2434	-1.372	-1.0817	-1.1507	0.5861	-0.8788	0.2667	0.4846	-0.3426	0.001	0.0014	0.1538	-0.0294	-0.008	-0.0088	32.6984	14.8557	46.9602
8	7.7852	0.0938	3.4039	1.3767	-1.1911	7.1562	-0.3238	0.3771	-0.1669	-0.4121	0.1981	-0.2417	-0.1551	0.2686	0.1258	-0.0918	-0.0056	0.0533	-0.1215	-0.0348	-0.094	31.9017	21.1722	41.5789
9	9.2655	-11.1702	3.543	18.3034	-7.6925	6.3869	-0.1683	-0.4749	0.0307	0.2451	-0.1195	-0.5931	0.1334	0.4464	0.2879	-0.1387	-0.0041	-0.0258	-0.0358	0.0223	-0.0901	34.7062	24.58	54.0621
10	8.231	-2.384	6.9945	23.475	-26.2033	31.5993	0.1447	0.0124	0.1147	0.0671	-0.1238	-0.2594	-0.2934	0.1094	-0.0209	-0.137	-0.0253	0.0332	-0.1333	-0.0622	-0.1374	27.3309	36.4797	44.588
11	45.7077	-8.6648	9.0531	39.4975	-37.5647	41.5881	0.6558	-0.2445	-1.2058	-0.4952	-0.4593	-0.3275	0.7081	-0.2601	-0.1964	-0.0826	-0.0204	0.0808	-0.1699	0.0009	-0.0816	23.6828	41.7826	36.9479
12	17.6276	-13.9579	5.3141	15.4225	-10.9216	43.3068	0.406	0.329	-0.2708	-0.7095	-0.0171	1.448	1.1726	-1.5601	-0.3889	-0.0854	-0.0211	-0.014	0.0451	0.111	0.0541	18.7516	47.5717	29.0147
13	7.6042	3.2404	-0.7742	15.8985	-2.2154	5.4226	0.0809	0.0987	0.7643	0.4914	0.071	0.0763	-0.7552	0.2552	-0.1519	-0.1004	-0.0029	0.0196	-0.104	0.0014	-0.1383	17.114	37.2848	56.6585
14	10.7578	4.9644	-4.3716	24.9119	-10.8828	23.5213	-0.1563	-0.1722	-0.6596	-0.1372	0.1386	-0.2216	0.5053	0.0453	0.0177	-0.1064	0.0091	0.015	-0.1282	-0.0313	-0.1861	14.6488	23.0039	60.1195
15	37.5236	11.783	-7.0488	6.5476	-4.9144	7.763	0.1115	-1.81	-1.1548	0.9366	-0.293	-0.3968	0.619	0.5969	0.1815	0.0053	0.0629	-0.008	-0.0138	-0.001	-0.1632	17.8479	26.0937	68.5326
16	24.4192	11.9953	-8.5726	14.9214	3.0605	9.4774	0.049	-0.2061	0.3323	0.5364	0.1755	-0.4477	-0.0004	0.9254	-0.2245	-0.0606	-0.0093	-0.0417	0.0104	-0.0964	-0.1652	25.4136	33.214	62.8401
17	11.7421	9.9119	-5.3385	13.2444	-4.924	9.2921	-0.1716	0.0534	0.2068	0.0574	0.3148	-0.4471	-0.2572	0.3088	-0.1432	-0.0977	0.0081	-0.037	-0.0798	-0.0674	-0.1774	20.3217	37.8449	68.9349
18	3.2501	-4.8299	-0.2117	9.2678	-4.6403	11.7602	-0.04	-0.402	-0.2095	0.3605	0.073	-0.1903	0.0015	0.1815	-0.0329	-0.0907	-0.028	0.0113	-0.0294	0.0003	-0.1818	9.6469	31.9615	75.1889
19	9.7243	2.6196	1.1413	6.0648	1.748	0.5212	0.0918	-0.361	0.5356	0.2872	-0.0141	-0.0612	-0.2288	0.0414	-0.0777	-0.0547	0.0184	-0.0148	-0.0354	-0.0335	-0.1277	10.0423	41.5489	67.1498
20	9.1207	3.6409	-0.5206	12.9111	-5.5148	8.1673	-0.2418	-0.0248	0.474	-0.2964	0.3712	0.5028	-0.4703	-0.4178	-0.1294	-0.0895	0.0263	-0.0324	-0.0766	0.0088	-0.1604	3.4031	37.8272	62.3444
21	6.3886	5.5624	-7.7849	6.5128	-5.7655	13.7276	0.0037	0.0738	0.0203	-0.1218	0.1907	0.3861	0.6703	-0.6432	-0.1945	-0.1437	-0.019	-0.0523	-0.0292	0.0086	-0.1134	4.9255	30.1311	58.2408
22	4.3944	9.9041	-1.7564	72.9884	-10.6325	14.3827	0.1304	0.0815	0.4855	0.9916	0.1257	0.4582	0.7089	-0.1508	-0.256	-0.0783	0.0418	0.0138	-0.0917	-0.0064	-0.1627	12.637	42.0158	47.7909
23	32.0484	14.1895	-15.9075	43.4613	-27.2741	29.3253	-0.0357	-0.038	-0.3703	0.1263	-0.474	-1.2357	0.7832	-0.1974	0.5097	-0.071	0.0593	0.015	-0.073	0.0102	-0.109	16.4737	47.8449	42.5947
24	13.2757	10.1137	-5.9617	36.9556	2.9488	4.5954	-0.4135	-0.3925	-0.1115	0.326	0.476	-1.6997	-0.2148	1.2576	-0.0624	-0.055	-0.0483	-0.0232	0.0388	0.1218	0.1008	20.0551	56.5188	39.2921

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	56 - 67
2	X-RAY DIFFRACTION	2	A	68 - 84
3	X-RAY DIFFRACTION	3	A	85 - 90
4	X-RAY DIFFRACTION	4	A	91 - 99
5	X-RAY DIFFRACTION	5	A	100 - 106
6	X-RAY DIFFRACTION	6	A	107 - 116
7	X-RAY DIFFRACTION	7	A	117 - 120
8	X-RAY DIFFRACTION	8	A	121 - 139
9	X-RAY DIFFRACTION	9	A	140 - 155
10	X-RAY DIFFRACTION	10	A	156 - 163
11	X-RAY DIFFRACTION	11	A	164 - 169
12	X-RAY DIFFRACTION	12	A	170 - 176
13	X-RAY DIFFRACTION	13	B	62 - 76
14	X-RAY DIFFRACTION	14	B	77 - 83
15	X-RAY DIFFRACTION	15	B	84 - 91
16	X-RAY DIFFRACTION	16	B	92 - 97
17	X-RAY DIFFRACTION	17	B	98 - 112
18	X-RAY DIFFRACTION	18	B	113 - 118
19	X-RAY DIFFRACTION	19	B	119 - 130
20	X-RAY DIFFRACTION	20	B	131 - 140
21	X-RAY DIFFRACTION	21	B	141 - 157
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