PDB-3c1q: The three-dimensional structure of the cytoplasmic domains of Eps...

ID or keywords:

Entry

Database: PDB / ID: 3c1q

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 / Type 2 Secretion System / T2SS / T4PB / Cholera / Inner membrane / Membrane / Transmembrane

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 /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Abendroth, J. / Mitchell, D.D. / Korotkov, K.V. / Kreeger, 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 24, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 3, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 30, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3c1q.cif.gz	71.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3c1q_validation.pdf.gz	719.7 KB	Display	wwPDB validaton report
Full document	3c1q_full_validation.pdf.gz	724.4 KB	Display
Data in XML	3c1q_validation.xml.gz	14.8 KB	Display
Data in CIF	3c1q_validation.cif.gz	21.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c1/3c1q ftp://data.pdbj.org/pub/pdb/validation_reports/c1/3c1q	HTTPS FTP

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Related structure data

Related structure data	2vmaSC 2vmbSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2vmb-d 2kxh-d 3qwn-3 5naz-d 4rv0-4 6pqb-4 6k6m-d 3h3p-2 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

28.6 kDa, 2 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)	46.988, 52.122, 89.470
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:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: TYR / End label comp-ID: TYR / End label seq-ID: 71 / Refine code: 6 / Auth seq-ID: 1 - 125

Dom-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID
1	CL	CL	A	D - A
2	CA	CA	B	G - B

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Protein , 1 types, 2 molecules AB

#1: Protein	General secretion pathway protein F / Cholera toxin secretion protein epsF Mass: 14031.403 Da / Num. of mol.: 2 / Fragment: cyto1-EpsF (UNP residues 56-170) Source method: isolated from a genetically manipulated source Details: C-terminal TEV-cleavable His-tag / Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: epsF / Plasmid: pACYC-CT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45780

#1: Protein

General secretion pathway protein F / Cholera toxin secretion protein epsF

Mass: 14031.403 Da / Num. of mol.: 2 / Fragment: cyto1-EpsF (UNP residues 56-170)
Source method: isolated from a genetically manipulated source
Details: C-terminal TEV-cleavable His-tag / Source: (gene. exp.)

Vibrio cholerae (bacteria) / Gene: epsF / Plasmid: pACYC-CT / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45780

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Non-polymers , 5 types, 340 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₉ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.95 Å³/Da / Density % sol: 36.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1ul protein at 10mg/ml + 1ul reservoir: 12.5% PEG 400, 200mM CaOAc2, 100mM MES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF
Detector	Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 30, 2006 / Details: multilayer (Varimax)
Radiation	Monochromator: multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 1.7→45.05 Å / Num. all: 23838 / Num. obs: 23838 / % possible obs: 95.6 % / Redundancy: 3.78 % / B_iso Wilson estimate: 17.5 Å² / R_merge(I) obs: 0.06 / R_sym value: 0.06 / Net I/σ(I): 15
Reflection shell	Resolution: 1.7→1.76 Å / Redundancy: 1.97 % / R_merge(I) obs: 0.223 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1347 / R_sym value: 0.223 / % possible all: 79.1

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Processing

Software

Name	Version	Classification
REFMAC	5.3.0021	refinement
CrystalClear		data collection
CrystalClear		data reduction
CrystalClear		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2vma, 2vmb

2vma

2vmb

Resolution: 1.7→33.94 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.94 / SU B: 3.737 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20793	1223	5.1 %	RANDOM
R_work	0.15587	-	-	-
all	0.15846	22632	-	-
obs	0.15846	22632	95.96 %	-

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: 9.193 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	0.48 Å²	0 Å²
3-	-	-	-0.48 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→33.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1808	0	20	335	2163

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1888
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1332
X-RAY DIFFRACTION	r_angle_refined_deg	1.274	2	2544
X-RAY DIFFRACTION	r_angle_other_deg	0.946	3.002	3220
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.925	5	243
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.167	23.488	86
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.964	15	356
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.622	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	289
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2084
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	375
X-RAY DIFFRACTION	r_nbd_refined	0.246	0.2	494
X-RAY DIFFRACTION	r_nbd_other	0.197	0.2	1407
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	966
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	958
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.181	0.2	227
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.109	0.2	9
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.235	0.2	20
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.27	0.2	74
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.241	0.2	43
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.089	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.519	1.5	1171
X-RAY DIFFRACTION	r_mcbond_other	0.163	1.5	471
X-RAY DIFFRACTION	r_mcangle_it	0.919	2	1885
X-RAY DIFFRACTION	r_scbond_it	1.998	3	724
X-RAY DIFFRACTION	r_scangle_it	3.178	4.5	652
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 803 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	loose positional	0.57	5
2	B	loose thermal	1.6	10

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.303	82	-
R_work	0.189	1347	-
obs	-	1347	78.91 %

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	0.9467	-0.1106	-0.02	0.6279	-0.2967	1.357	-0.0005	0.0897	0.0053	-0.0623	0.0333	0.0219	0.0408	0.0093	-0.0327	0.0497	0.007	-0.0075	0.058	0.0055	0.0423	22.2585	24.3905	45.3776
2	3.7566	-0.4597	1.1537	0.0711	-0.0443	3.5867	-0.1329	-0.0341	-0.104	0.0261	0.0305	0.0827	0.0316	-0.1789	0.1025	0.0519	-0.0102	-0.0001	0.0211	-0.0174	0.0545	15.9687	18.4111	49.0719
3	4.2986	-0.8431	1.252	1.3752	-1.6383	6.7424	-0.2152	0.1318	-0.4054	-0.0756	0.1049	-0.0271	0.1413	0.147	0.1102	0.0538	-0.0326	0.0462	-0.0062	-0.0277	0.0718	22.1175	11.3681	46.4727
4	2.6881	0.8085	0.0483	1.1932	-0.2624	1.4821	-0.0711	0.0723	-0.0543	-0.066	0.0563	0.0005	0.0872	0.1388	0.0148	0.032	0.0054	0.0085	0.0286	-0.0031	0.0462	31.9046	18.7184	44.9434
5	2.1991	-1.9689	0.3061	4.8848	-2.1887	3.2394	-0.0505	0.0076	0.1466	0.0935	-0.0556	-0.1706	0.0353	0.1989	0.1061	0.0287	-0.008	0.0117	0.0375	-0.0028	0.069	29.3325	29.5888	51.149
6	2.709	-1.4724	1.0652	9.4873	-5.8335	8.5568	-0.0391	0.1414	-0.2282	-0.1251	0.0974	-0.0813	0.2335	-0.1393	-0.0583	0.0515	-0.0014	0.0373	0.0155	-0.0106	0.0169	22.3512	42.8432	38.0198
7	1.6235	0.0446	0.1127	5.1366	-2.2363	2.3857	-0.0196	0.0031	0.0661	0.1312	0.0198	0.0224	-0.0908	0.0338	-0.0002	0.0421	0.0049	0.0028	0.0444	-0.0039	0.0275	14.8797	30.8944	59.0523
8	4.1069	1.4746	-1.1035	5.5564	1.332	2.5694	-0.0103	-0.2388	0.0202	0.1298	0.1339	-0.2386	-0.0916	0.1965	-0.1236	0.0564	0.0115	-0.0368	0.0901	-0.0177	0.0094	21.7256	32.0639	65.6565
9	4.2767	3.7975	-2.4008	6.3994	-1.8264	5.359	0.0173	-0.1669	-0.1678	0.255	-0.0164	-0.1462	-0.001	0.0455	-0.0009	0.0438	0.0096	-0.0343	0.077	-0.0254	0.0123	16.866	33.8437	72.0429
10	1.8232	0.3288	0.7155	1.3161	0.9232	2.1773	-0.0214	-0.143	0.1313	-0.0298	-0.0196	0.1408	-0.0913	-0.2702	0.0411	0.0379	0.0023	0.0038	0.0504	-0.0064	0.0248	5.1256	34.7962	65.9882
11	3.7286	3.5884	-1.7071	6.8405	-3.5551	4.2643	0.0466	0.0578	0.1488	-0.074	0.0522	0.1038	-0.1518	-0.0687	-0.0988	0.0375	0.0083	-0.0113	0.0185	0.0132	0.0493	9.0271	34.9175	52.2777
12	3.1714	2.971	-2.4365	8.8641	-2.6867	5.1628	-0.0927	-0.0832	-0.0315	-0.1953	0.0918	-0.1092	0.0854	0.1195	0.0009	0.0073	0.0147	0.0084	0.0523	0.0116	0.0435	17.4258	49.448	41.6722

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	57 - 83	3 - 29
2	X-RAY DIFFRACTION	2	A	A	84 - 102	30 - 48
3	X-RAY DIFFRACTION	3	A	A	103 - 115	49 - 61
4	X-RAY DIFFRACTION	4	A	A	116 - 144	62 - 90
5	X-RAY DIFFRACTION	5	A	A	145 - 161	91 - 107
6	X-RAY DIFFRACTION	6	A	A	162 - 171	108 - 117
7	X-RAY DIFFRACTION	7	B	B	63 - 85	9 - 31
8	X-RAY DIFFRACTION	8	B	B	86 - 100	32 - 46
9	X-RAY DIFFRACTION	9	B	B	101 - 114	47 - 60
10	X-RAY DIFFRACTION	10	B	B	115 - 149	61 - 95
11	X-RAY DIFFRACTION	11	B	B	150 - 161	96 - 107
12	X-RAY DIFFRACTION	12	B	B	162 - 177	108 - 123

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Non-polymers , 5 types, 340 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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Yorodumi