PDB-4kss: Crystal Structure of Vibrio cholerae ATPase GspsE Hexamer

ID or keywords:

Entry

Database: PDB / ID: 4kss

Title

Crystal Structure of Vibrio cholerae ATPase GspsE Hexamer

Components

Type II secretion system protein E, hemolysin-coregulated protein

Keywords

PROTEIN TRANSPORT / T2SS secretion ATPase / EpsE / Hexamer / Quasi C6 cyclic symmetry

Function / homology

Function and homology information

protein-exporting ATPase activity / protein-secreting ATPase / protein secretion by the type II secretion system / type II protein secretion system complex / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Vibrio cholerae O1 (bacteria)

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

molecular replacement / Resolution: 7.58 Å

Authors

Hol, W.G. / Turley, S. / Lu, C.Y. / Park, Y.J.

Citation

Journal: Structure / Year: 2013
Title: Hexamers of the Type II Secretion ATPase GspE from Vibrio cholerae with Increased ATPase Activity.
Authors: Lu, C. / Turley, S. / Marionni, S.T. / Park, Y.J. / Lee, K.K. / Patrick, M. / Shah, R. / Sandkvist, M. / Bush, M.F. / Hol, W.G.

History

Deposition	May 17, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 4, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2013	Group: Database references
Revision 1.2	Aug 23, 2017	Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4kss.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4kss.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	4kss.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4kss_validation.pdf.gz	493 KB	Display	wwPDB validaton report
Full document	4kss_full_validation.pdf.gz	524.6 KB	Display
Data in XML	4kss_validation.xml.gz	104.4 KB	Display
Data in CIF	4kss_validation.cif.gz	137.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ks/4kss ftp://data.pdbj.org/pub/pdb/validation_reports/ks/4kss	HTTPS FTP

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Related structure data

Related structure data	4ksrC C: citing same article (ref.)
Similar structure data	7476 6kph-d 3o44-2 3j94-d 0752 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: Type II secretion system protein E, hemolysin-coregulated protein

B: Type II secretion system protein E, hemolysin-coregulated protein

C: Type II secretion system protein E, hemolysin-coregulated protein

D: Type II secretion system protein E, hemolysin-coregulated protein

E: Type II secretion system protein E, hemolysin-coregulated protein

F: Type II secretion system protein E, hemolysin-coregulated protein

384 kDa, 6 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)	205.064, 205.064, 234.983
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2

#1: Protein	Type II secretion system protein E, hemolysin-coregulated protein / T2SS protein E / Cholera toxin secretion protein EpsE / General secretion pathway protein E / Type ...T2SS protein E / Cholera toxin secretion protein EpsE / General secretion pathway protein E / Type II traffic warden ATPase Mass: 63927.793 Da / Num. of mol.: 6 / Fragment: T2SS EpsE, P37093 residues 100-503, Q02UZ4 Source method: isolated from a genetically manipulated source Details: Chimeric Protein Source: (gene. exp.) Vibrio cholerae O1 (bacteria), (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961, UCBPP-PA14 / Gene: epsE, VC_2732, PA14_01030 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37093, UniProt: Q02UZ4

#1: Protein

Type II secretion system protein E, hemolysin-coregulated protein / T2SS protein E / Cholera toxin secretion protein EpsE / General secretion pathway protein E / Type ...

Mass: 63927.793 Da / Num. of mol.: 6 / Fragment: T2SS EpsE, P37093 residues 100-503, Q02UZ4
Source method: isolated from a genetically manipulated source
Details: Chimeric Protein
Source: (gene. exp.)

Vibrio cholerae O1 (bacteria), (gene. exp.)

Pseudomonas aeruginosa (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961, UCBPP-PA14 / Gene: epsE, VC_2732, PA14_01030 / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37093, UniProt: Q02UZ4

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.22 Å³/Da / Density % sol: 61.8 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 7% PEG6000, 0.1M Bicine, 5mM ADP, 5mM MgCl2, 5 mM AMPPNP, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å

Detector

Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 31, 2013

Radiation

Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.542 Å / Relative weight: 1

Reflection

Redundancy: 6.7 % / Av σ(I) over netI: 6.35 / Number: 56324 / R_merge(I) obs: 0.24 / Χ²: 1.18 / D res high: 7 Å / D res low: 90 Å / Num. obs: 8382 / % possible obs: 99.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
15.06	90	94.9	1	0.089	1.392	6.1
11.96	15.06	99.4	1	0.169	1.237	6.8
10.45	11.96	99.6	1	0.189	1.199	6.8
9.5	10.45	99.6	1	0.232	1.161	6.8
8.82	9.5	99.9	1	0.335	1.144	6.8
8.3	8.82	100	1	0.506	1.121	6.8
7.88	8.3	100	1	0.814	1.131	6.8
7.54	7.88	100	1		1.086	6.8
7.25	7.54	100	1		1.115	6.8
7	7.25	100	1		1.198	6.8

Reflection

Resolution: 7→90 Å / Num. obs: 8382 / % possible obs: 99.3 % / Redundancy: 6.7 % / R_merge(I) obs: 0.24 / Χ²: 1.178 / Net I/σ(I): 3

Reflection shell

Resolution (Å)	Redundancy (%)	Num. unique all	Χ²	Diffraction-ID	% possible all	R_merge(I) obs
7-7.25	6.8	828	1.198	1	100
7.25-7.54	6.8	803	1.115	1	100
7.54-7.88	6.8	831	1.086	1	100
7.88-8.3	6.8	825	1.131	1	100	0.814
8.3-8.82	6.8	821	1.121	1	100	0.506
8.82-9.5	6.8	842	1.144	1	99.9	0.335
9.5-10.45	6.8	836	1.161	1	99.6	0.232
10.45-11.96	6.8	840	1.199	1	99.6	0.189
11.96-15.06	6.8	861	1.237	1	99.4	0.169
15.06-90	6.1	895	1.392	1	94.9	0.089

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Resolution: 7.58→50 Å / Cor.coef. F_o:F_c: 0.673 / Cor.coef. F_o:F_c free: 0.669 / SU ML: 3.953 / Cross valid method: THROUGHOUT / ESU R Free: 5.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.35989	308	4.7 %	RANDOM
R_work	0.34875	-	-	-
obs	0.34924	6265	99.05 %	-

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: 164.076 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.16 Å²	-0 Å²	0 Å²
2-	-	-2.16 Å²	0 Å²
3-	-	-	4.32 Å²

Refinement step

Cycle: LAST / Resolution: 7.58→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24126	0	0	0	24126

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.037	0.019	24462
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	24270
X-RAY DIFFRACTION	r_angle_refined_deg	1.723	1.974	32982
X-RAY DIFFRACTION	r_angle_other_deg	3.611	3.001	55800
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.327	5	3090
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.259	23.966	1044
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.916	15	4572
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.136	15	204
X-RAY DIFFRACTION	r_chiral_restr	0.049	0.2	3846
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	27252
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	5220
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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

LS refinement shell

Resolution: 7.58→7.776 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.353	29	-
R_work	0.343	432	-
obs	-	-	98.09 %

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	15.6871	-12.3926	-6.7436	15.9976	0.293	7.6783	2.1359	1.5074	-1.6092	-0.8715	-2.5009	2.3704	-1.784	-0.122	0.365	1.7075	-0.0213	0.0294	2.1679	-0.3275	1.083	-73.1135	-96.3974	-8.3434
2	17.8669	2.8024	2.4792	7.4935	0.1128	2.3111	-0.4531	-0.7226	0.3053	-0.3089	-0.1471	1.2909	-0.1886	0.3926	0.6002	0.7499	-0.0079	0.139	0.8972	0.1648	0.4868	-95.8394	-57.3634	-21.392
3	16.8528	-2.2029	-0.2873	1.3781	4.8536	21.5284	-1.5198	-2.3622	1.444	0.0766	0.5465	-0.033	-0.0458	0.8774	0.9733	1.1313	0.0318	0.5927	0.6998	0.0324	1.1241	-73.335	-17.4773	-25.041
4	6.1813	1.6103	3.9192	7.3815	7.8069	9.543	1.2684	-0.0182	-0.4929	0.4678	-1.0792	0.5251	1.4944	-1.5276	-0.1892	2.1268	-0.3425	-0.0764	1.1569	0.0968	1.6283	-49.3336	-95.1462	-27.3859
5	7.2973	-0.7239	4.773	5.326	-2.5251	19.6565	0.0692	0.2942	-0.1699	-1.3989	-0.8053	0.1192	-0.3861	-1.7334	0.7361	1.0708	0.072	0.1522	0.5617	-0.2831	0.9663	-77.6	-76.156	-37.4191
6	8.813	2.4626	-6.5155	10.9257	-10.4744	13.1563	0.1575	1.0408	0.6276	-1.1213	-0.3355	0.0929	-0.6071	0.0665	0.178	2.3454	-0.3774	-0.6728	1.5744	-0.1029	0.5977	-73.7608	-41.0293	-43.8463
7	4.7069	-0.5999	0.419	6.1258	-0.9117	2.2235	0.3119	-0.626	0.2942	0.311	-0.048	0.5203	-0.3033	-0.181	-0.2639	1.1843	-0.2079	0.1824	1.1528	-0.2296	0.8002	-39.5695	-69.3017	-78.0015
8	8.1742	-0.8559	0.967	1.8534	0.2896	15.0244	-0.5645	-0.37	0.491	0.2011	0.2222	-0.3494	-0.1741	-0.2019	0.3423	0.8641	0.0694	0.0762	0.2484	-0.4105	0.7219	-27.6078	-15.0802	-15.9725
9	0.9055	3.2069	0.5545	14.9274	0.1562	7.3308	-0.1003	-0.0885	-0.1453	0.7601	-0.6054	-0.599	-0.4005	0.1369	0.7056	0.6357	0.0861	-0.2893	0.8146	-0.2397	0.461	-4.8833	-53.6165	-3.2378
10	14.2772	-11.7863	-11.952	18.0542	1.0635	19.4555	-0.7699	2.0579	0.6086	1.2067	-1.0884	-2.6711	-0.4414	-2.1649	1.8583	1.5107	0.0106	-0.5489	1.9727	0.4377	0.9258	-27.4879	-93.7664	0.8356
11	13.3224	2.5023	-9.0912	4.618	-4.1035	9.3368	0.8655	-1.6888	0.5186	-0.86	-0.5671	-0.8758	-0.9822	2.6517	-0.2984	1.5729	-0.3238	0.5172	1.5798	-0.4006	1.482	-42.1377	-25.7269	-40.6238
12	15.0425	-5.4726	-7.9933	7.2791	7.0372	7.5044	-1.6689	-1.0174	-1.0925	1.0119	1.9226	-0.5399	1.2642	1.9967	-0.2537	1.2368	0.4421	-0.2428	1.6872	-0.1655	1.2848	-14.0563	-44.7025	-30.7904
13	3.4956	0.3703	-1.1408	13.8702	8.9486	9.0515	-1.417	-0.0139	-0.8939	0.9497	1.1066	-0.4737	2.2638	0.6507	0.3104	1.3508	0.4367	0.0583	1.0759	-0.1952	1.139	-17.7303	-79.5632	-24.1745

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	121 - 229
2	X-RAY DIFFRACTION	2	B	121 - 229
3	X-RAY DIFFRACTION	3	C	121 - 229
4	X-RAY DIFFRACTION	4	A	235 - 500
5	X-RAY DIFFRACTION	5	B	235 - 500
6	X-RAY DIFFRACTION	6	C	235 - 500
7	X-RAY DIFFRACTION	7	A	511 - 671
8	X-RAY DIFFRACTION	7	B	511 - 671
9	X-RAY DIFFRACTION	7	C	511 - 671
10	X-RAY DIFFRACTION	7	D	511 - 671
11	X-RAY DIFFRACTION	7	E	511 - 671
12	X-RAY DIFFRACTION	7	F	511 - 671
13	X-RAY DIFFRACTION	8	D	121 - 229
14	X-RAY DIFFRACTION	9	E	121 - 229
15	X-RAY DIFFRACTION	10	F	121 - 229
16	X-RAY DIFFRACTION	11	D	235 - 500
17	X-RAY DIFFRACTION	12	E	235 - 500
18	X-RAY DIFFRACTION	13	F	235 - 500

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