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

ID or keywords:

Entry

Database: PDB / ID: 2vma

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 /

SAD / Resolution: 1.9 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	Oct 9, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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_entry_details.has_protein_modification / _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.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_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	2vma.cif.gz	66.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2vma.ent.gz	50.5 KB	Display	PDB format
PDBx/mmJSON format	2vma.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2vma_validation.pdf.gz	436.4 KB	Display	wwPDB validaton report
Full document	2vma_full_validation.pdf.gz	438.3 KB	Display
Data in XML	2vma_validation.xml.gz	16 KB	Display
Data in CIF	2vma_validation.cif.gz	21.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vm/2vma ftp://data.pdbj.org/pub/pdb/validation_reports/vm/2vma	HTTPS FTP

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Related structure data

Related structure data	2vmbC 3c1qC C: citing same article (ref.)
Similar structure data	2d9x-d 5kqb-d 3gef-1 2vmb-1 3gef-3 2da0-d 2mfq-d 3ihx-1 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

30.1 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
14.8 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
15.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.816, 54.368, 88.587
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	5	A	56 - 177
2	1	1	5	B	56 - 177

NCS oper: (Code: given
Matrix: (-0.99988, 0.00497, -0.01461), (0.01517, 0.14604, -0.98916), (-0.00278, -0.98927, -0.14609)
Vector: 39.49799, 78.3618, 91.27634)

#1: Protein	GENERAL SECRETION PATHWAY PROTEIN F / EPSF / CHOLERA TOXIN SECRETION PROTEIN EPSF Mass: 14028.238 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) / References: UniProt: P45780
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
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: ROTATING ANODE / Wavelength: 1.5418
Detector	Type: RIGAKU CCD / Detector: CCD / Date: Oct 23, 2006 / Details: MIRRORS
Radiation	Monochromator: OSMIC VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.9→48.82 Å / Num. obs: 18609 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 12.11 % / R_merge(I) obs: 0.09 / Net I/σ(I): 16.1
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.33 / Mean I/σ(I) obs: 3.9 / % possible all: 77.2

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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: 1.9→46.32 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.933 / SU B: 6.078 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.255	946	5.1 %	RANDOM
R_work	0.208	-	-	-
obs	0.21	17615	96.6 %	-

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: 17.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.07 Å²	0 Å²	0 Å²
2-	-	1.74 Å²	0 Å²
3-	-	-	-1.67 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→46.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1836	0	18	215	2069

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1895
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	1346
X-RAY DIFFRACTION	r_angle_refined_deg	1.211	1.988	2557
X-RAY DIFFRACTION	r_angle_other_deg	0.969	3	3276
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.439	5	242
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.891	23.409	88
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.077	15	360
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.087	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	289
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2098
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	378
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	438
X-RAY DIFFRACTION	r_nbd_other	0.186	0.2	1362
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	925
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	982
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.221	0.2	147
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	0.239	0.2	26
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.261	0.2	68
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.254	0.2	14
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	0.639	1.5	1192
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.953	2	1898
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.906	3	744
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.003	4.5	654
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

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

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	652	medium positional	0.19	0.5
2	B	652	medium positional	0.19	0.5
1	A	785	loose positional	0.69	5
2	B	785	loose positional	0.69	5
1	A	652	medium thermal	0.67	2
2	B	652	medium thermal	0.67	2
1	A	785	loose thermal	1.29	10
2	B	785	loose thermal	1.29	10

LS refinement shell

Resolution: 1.9→1.95 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.321	50	-
R_work	0.278	1002	-
obs	-	-	74.5 %

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	0.1794	0.403	0.7275	1.225	2.3066	4.3642	-0.0538	-0.0323	0.0622	-0.1173	0.1604	0.0944	-0.1627	0.2558	-0.1067	0.0583	-0.0245	0.0016	0.0663	0.0087	0.0383	22.9973	25.7339	39.2542
2	2.6662	-0.5511	0.3992	0.2037	0.0096	2.0895	-0.1041	-0.1617	-0.124	-0.0034	0.0857	0.0102	0.1115	-0.0509	0.0184	0.0771	0.0082	-0.0024	0.051	0.001	0.0177	19.0862	20.2629	51.7163
3	3.2031	-1.4414	3.9011	5.053	-3.193	5.2203	-0.2102	0.1694	-0.3699	-0.1638	0.1664	-0.1309	0.1749	-0.2256	0.0438	0.0947	-0.0326	0.0699	0.0347	-0.021	0.0665	21.9516	12.7548	45.6548
4	1.6612	0.6433	0.7305	1.9761	0.0661	1.2009	-0.1973	0.2011	-0.1418	-0.1201	0.0773	-0.1019	0.1512	0.0729	0.1201	0.0843	-0.0208	0.0573	0.073	-0.0326	0.0413	31.0516	19.1509	41.5851
5	0.6485	0.3843	-0.5022	0.6328	-0.7931	2.0861	-0.1557	-0.2439	0.1157	0.028	0.0891	-0.1456	-0.0183	0.2169	0.0665	0.0374	0.0202	-0.0023	0.0985	-0.0159	0.0637	34.8941	24.0056	53.0965
6	2.7852	-5.7762	6.5859	12.4338	-13.2194	15.997	0.0881	-0.1333	0.0662	-0.0169	0.078	0.025	0.0738	-0.2596	-0.1661	-0.0157	-0.0051	0.0445	0.0777	0.0204	0.0634	23.3263	42.3678	37.7375
7	0.9115	-0.1621	0.2112	3.6436	-2.2721	2.0507	-0.069	0.0336	0.0772	0.0482	0.1366	-0.0579	0.059	0.0025	-0.0675	0.0497	0.023	0.0049	0.1053	-0.013	0.0283	15.7786	30.3336	58.5246
8	2.0332	0.8128	-0.2081	1.009	0.9118	1.4685	-0.0029	-0.1984	0.0463	0.0405	0.1339	-0.0828	0.1159	0.3181	-0.131	0.0752	0.0139	-0.022	0.1334	-0.0221	-0.0015	20.1279	34.5945	68.187
9	1.1307	0.8469	1.0729	1.0893	-0.3256	3.8203	-0.0095	-0.1006	0.1767	-0.0021	-0.0474	0.1213	-0.1652	-0.1212	0.0569	0.0625	0.0123	0.0091	0.0733	-0.007	0.0275	7.9304	40.6201	66.038
10	0.5158	0.4186	0.0445	0.605	0.7646	2.0039	0.0888	0.1148	-0.0329	-0.0271	-0.1089	-0.0253	0.2103	-0.3999	0.0202	0.0758	-0.0341	-0.0201	0.126	-0.0037	0.0207	3.9517	30.084	59.7335
11	3.9729	5.8337	-4.4721	15.2019	-13.953	13.2554	-0.2564	-0.134	0.3418	0.1257	0.0336	-0.1935	0.2205	-0.1029	0.2228	0.0292	0.0235	0.0021	0.0681	0.0108	0.0543	11.7669	39.7585	48.2107
12	2.3701	4.0506	0.1588	16.7125	-8.2238	7.3821	-0.1318	-0.154	-0.2879	-0.2562	-0.1535	-0.8064	0.3366	0.6455	0.2854	-0.0273	0.0378	0.035	0.0514	-0.003	0.1049	18.3954	53.4478	40.6058

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	56 - 76
2	X-RAY DIFFRACTION	2	A	77 - 101
3	X-RAY DIFFRACTION	3	A	102 - 115
4	X-RAY DIFFRACTION	4	A	116 - 135
5	X-RAY DIFFRACTION	5	A	136 - 154
6	X-RAY DIFFRACTION	6	A	155 - 177
7	X-RAY DIFFRACTION	7	B	66 - 85
8	X-RAY DIFFRACTION	8	B	86 - 115
9	X-RAY DIFFRACTION	9	B	116 - 135
10	X-RAY DIFFRACTION	10	B	136 - 154
11	X-RAY DIFFRACTION	11	B	155 - 163
12	X-RAY DIFFRACTION	12	B	164 - 177

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