PDB-2w7v: periplasmic domain of EpsL from Vibrio parahaemolyticus

ID or keywords:

Entry

Database: PDB / ID: 2w7v

Title

periplasmic domain of EpsL from Vibrio parahaemolyticus

Components

GENERAL SECRETION PATHWAY PROTEIN L

Keywords

TRANSPORT PROTEIN / TRANSPORT / TYPE II SECRETION

Function / homology

Function and homology information

Gram-negative-bacterium-type cell wall / protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane
Similarity search - Function

Biological species

VIBRIO PARAHAEMOLYTICUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Abendroth, J. / Kreger, A.C. / Abendroth, H. / Sandkvist, M. / Hol, W.G.J.

Citation

Journal: J.Struct.Biol. / Year: 2009
Title: The Dimer Formed by the Periplasmic Domain of Epsl from the Type 2 Secretion System of Vibrio Parahaemolyticus.
Authors: Abendroth, J. / Kreger, A.C. / Hol, W.G.J.

History

Deposition	Jan 6, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 31, 2010	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 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / 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 / struct_conn / struct_ncs_dom_lim / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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	2w7v.cif.gz	49.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2w7v.ent.gz	36.8 KB	Display	PDB format
PDBx/mmJSON format	2w7v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2w7v_validation.pdf.gz	442.7 KB	Display	wwPDB validaton report
Full document	2w7v_full_validation.pdf.gz	443.9 KB	Display
Data in XML	2w7v_validation.xml.gz	9.7 KB	Display
Data in CIF	2w7v_validation.cif.gz	12.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w7/2w7v ftp://data.pdbj.org/pub/pdb/validation_reports/w7/2w7v	HTTPS FTP

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Related structure data

Similar structure data	3rio-d 6lhy-2 1sx2-d 6y2c-d 3kes-2 3rlb-2 2xv6-1 6tqr-2 2ggz-2 6u3l-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

Deposited unit

A: GENERAL SECRETION PATHWAY PROTEIN L

B: GENERAL SECRETION PATHWAY PROTEIN L

hetero molecules

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

1

A: GENERAL SECRETION PATHWAY PROTEIN L

hetero molecules

A: GENERAL SECRETION PATHWAY PROTEIN L

hetero molecules

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

2

B: GENERAL SECRETION PATHWAY PROTEIN L

hetero molecules

B: GENERAL SECRETION PATHWAY PROTEIN L

hetero molecules

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

Unit cell

Length a, b, c (Å)	87.712, 87.712, 45.589
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	171
Space group name H-M	P6₂

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 322 - 404 / Label seq-ID: 5 - 87

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

NCS oper: (Code: given
Matrix: (0.5001, 0.866, 3.0E-6), (0.866, -0.5001, 0.00044), (0.000383, -0.000217, -1)
Vector: 0.00072, -0.00327, 15.2099)

#1: Protein	GENERAL SECRETION PATHWAY PROTEIN L Mass: 10911.814 Da / Num. of mol.: 2 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 319-404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VIBRIO PARAHAEMOLYTICUS (bacteria) / Plasmid: PJA-080 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21GOLD(DE3) / References: UniProt: Q87TC9
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	PERIPLASMIC DOMAIN SER319-GLN404, M318 IS A CLONING ARTEFACT, THE C-TERMINAL HIS6-TAG SEQUENCE ...PERIPLASMIC DOMAIN SER319-GLN404, M318 IS A CLONING ARTEFACT, THE C-TERMINAL HIS6-TAG SEQUENCE LEHHHHHH ORIGINATES FROM THE VECTOR

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.57 Å³/Da / Density % sol: 51.8 % / Description: NONE
Crystal grow	Details: 1.2-1.4M NA/K PHOSPHATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97924
Detector	Type: ADSC CCD / Detector: CCD / Date: Jul 14, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97924 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 9031 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.3 % / R_merge(I) obs: 0.08 / Net I/σ(I): 18.1
Reflection shell	Resolution: 2.3→2.35 Å / Redundancy: 11.3 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM		phasing
ARP/wARP		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2.3→39.1 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.921 / SU B: 16.714 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.256	426	4.7 %	RANDOM
R_work	0.214	-	-	-
obs	0.216	8585	100 %	-

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: 12.59 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.12 Å²	-0.56 Å²	0 Å²
2-	-	-1.12 Å²	0 Å²
3-	-	-	1.69 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→39.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1300	0	18	50	1368

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	1378
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	976
X-RAY DIFFRACTION	r_angle_refined_deg	1.615	1.946	1854
X-RAY DIFFRACTION	r_angle_other_deg	0.931	3	2354
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.509	5	168
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.493	23.429	70
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.546	15	250
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.54	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	200
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1512
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	298
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	262
X-RAY DIFFRACTION	r_nbd_other	0.206	0.2	971
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	633
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	810
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.192	0.2	60
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	0.253	0.2	26
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.191	0.2	49
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.283	0.2	11
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	0.863	1.5	1002
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.111	2	1318
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.997	3	624
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.892	4.5	532
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 / Number: 1152 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.02	0.05
2	B	tight positional	0.02	0.05
1	A	tight thermal	0.07	0.5
2	B	tight thermal	0.07	0.5

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_work	0.246	637
R_free	-	0

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	43.8406	-11.1909	-6.0796	60.5425	29.9639	55.4547	1.5952	0.4844	2.8894	2.0143	1.0705	-1.9142	-1.7566	3.4054	-2.6657	0.2615	-0.0817	0.1163	0.2941	-0.0138	0.2539	33.7064	42.4547	1.5741
2	11.9394	7.3321	1.4545	12.4126	4.4466	1.7735	0.8854	-0.3635	-0.9905	1.9252	-0.216	-1.2643	-0.4341	-0.5193	-0.6694	0.5328	0.1461	-0.2117	0.25	0.0365	0.2015	25.9806	34.4122	-4.0395
3	4.6542	-0.4006	-0.2686	27.551	6.1049	11.2064	-0.2358	0.6447	-0.1973	-0.4583	-0.0575	1.3671	-0.0519	-0.6473	0.2933	0.1827	0.0841	-0.0572	0.3556	0.0793	0.3539	17.1087	25.9714	1.0073
4	39.1836	1.6295	0.2405	51.0066	1.6513	2.8642	0.2917	-1.7851	0.0581	2.2003	0.3066	-2.7952	0.0007	0.4157	-0.5983	0.2414	0.0998	-0.1462	0.2629	-0.0884	0.2437	30.5008	39.0889	8.1604
5	7.132	2.7307	-1.2764	11.4169	-1.5115	3.5768	0.2188	0.1101	-0.0692	0.119	-0.1079	0.3805	0.5183	-0.1029	-0.1109	0.2411	0.097	-0.0892	0.2133	0.0099	0.2574	22.3221	21.867	4.0327
6	7.1851	4.6378	-7.1991	25.3544	-9.4699	8.2535	-0.8558	0.5015	0.3005	-1.0408	0.3703	-0.6596	-0.3532	0.305	0.4855	0.1799	0.0667	-0.0113	0.2639	-0.0067	0.2835	32.134	26.8551	-0.6278
7	54.3265	13.5492	-16.4227	9.2103	-4.1123	13.6386	0.1323	-1.0159	-0.6407	0.719	-0.1003	0.8564	0.4185	-0.389	-0.032	0.3088	0.1161	0.0551	0.1955	0.0768	0.3776	19.3894	17.9356	12.0112
8	25.0683	14.7236	-7.6483	22.403	-8.6111	16.0087	0.0944	-0.0047	0.7758	0.2482	-0.0271	-0.6459	0.1041	0.759	-0.0673	0.3335	0.2168	-0.0436	0.2967	-0.0164	0.4477	29.8807	28.7889	5.0565
9	53.9145	-2.1129	-8.8272	43.7343	14.9371	56.9748	1.9214	2.212	0.3112	-0.0805	0.3013	-2.8062	-2.3922	3.069	-2.2227	0.2353	-0.0441	0.0193	0.287	-0.0809	0.2331	53.6181	7.9617	13.6444
10	18.6784	1.5853	-0.9883	4.2264	2.57	1.7736	1.1181	2.0357	2.2834	-0.2763	-0.0952	0.196	0.4828	0.1375	-1.0228	0.4063	0.1912	0.1425	0.2688	0.2143	0.2897	43.633	5.3838	19.4693
11	19.2159	-10.6808	-4.2997	12.7296	3.4051	14.7542	0.1351	-0.098	-0.3073	0.7137	-0.1255	0.3541	0.4212	-0.649	-0.0095	0.3889	-0.0314	-0.0367	0.1131	0.0628	0.3223	31.2977	2.0317	14.4504
12	46.5361	-4.8538	-1.8517	34.2686	-0.0233	3.2817	0.3836	2.1035	1.8952	-1.5988	0.2586	-1.0889	-0.5729	0.3773	-0.6422	0.3225	0.0225	0.1389	0.1819	0.0553	0.2701	49.1009	6.8745	7.0501
13	13.2635	0.2802	2.4037	5.5173	-0.2566	4.0258	-0.0376	0.0448	-0.4587	0.2025	0.1545	0.3007	-0.2272	-0.5132	-0.1169	0.323	0.0446	0.0387	0.1442	0.0794	0.2163	30.0986	8.3972	11.1828
14	26.0954	-9.4984	12.3668	15.2574	-1.1491	7.8841	-0.2333	-1.3621	0.5128	0.4111	-0.2151	-0.97	-0.5089	0.3787	0.4485	0.2577	-0.0286	-0.0106	0.1317	0.0043	0.2933	39.3315	14.3939	15.8437
15	32.312	25.0883	9.3446	26.8386	8.319	11.777	-0.0321	1.2797	-0.7629	-0.477	0.4598	0.7245	0.1547	-0.609	-0.4277	0.3233	0.1165	-0.0924	0.1967	-0.0388	0.4166	25.2232	7.8254	3.2143
16	33.5078	9.0552	10.1104	12.4065	2.2105	15.7721	-0.2089	0.2431	0.4273	-0.1389	0.0635	-0.7793	-0.9022	0.2764	0.1453	0.493	0.1416	0.0028	0.153	0.0192	0.4437	39.8673	11.4824	10.1722

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	322 - 327
2	X-RAY DIFFRACTION	2	A	328 - 338
3	X-RAY DIFFRACTION	3	A	339 - 349
4	X-RAY DIFFRACTION	4	A	350 - 357
5	X-RAY DIFFRACTION	5	A	358 - 376
6	X-RAY DIFFRACTION	6	A	377 - 384
7	X-RAY DIFFRACTION	7	A	385 - 395
8	X-RAY DIFFRACTION	8	A	396 - 404
9	X-RAY DIFFRACTION	9	B	322 - 327
10	X-RAY DIFFRACTION	10	B	328 - 337
11	X-RAY DIFFRACTION	11	B	338 - 349
12	X-RAY DIFFRACTION	12	B	350 - 357
13	X-RAY DIFFRACTION	13	B	358 - 376
14	X-RAY DIFFRACTION	14	B	377 - 384
15	X-RAY DIFFRACTION	15	B	385 - 395
16	X-RAY DIFFRACTION	16	B	396 - 404

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