PDB-3kvn: Crystal structure of the full-length autotransporter EstA from Ps...

ID or keywords:

Entry

Database: PDB / ID: 3kvn

Title

Crystal structure of the full-length autotransporter EstA from Pseudomonas aeruginosa

Components

Esterase estA

Keywords

HYDROLASE / beta barrel / alpha-beta-alpha motif / Cell membrane / Cell outer membrane / Membrane / Transmembrane

Function / homology

Function and homology information

glycolipid biosynthetic process / lipase activity / carboxylesterase / carboxylesterase activity / bacterial-type flagellum-dependent swarming motility / single-species biofilm formation / carboxylic ester hydrolase activity / lipid biosynthetic process / bacterial-type flagellum-dependent cell motility / cell motility / cell outer membrane
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.499 Å

Authors

van den Berg, B.

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of a full-length autotransporter.
Authors: van den Berg, B.

History

Deposition	Nov 30, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 26, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _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	3kvn.cif.gz	496.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3kvn.ent.gz	410.4 KB	Display	PDB format
PDBx/mmJSON format	3kvn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3kvn_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	3kvn_full_validation.pdf.gz	1.6 MB	Display
Data in XML	3kvn_validation.xml.gz	57.5 KB	Display
Data in CIF	3kvn_validation.cif.gz	77.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kv/3kvn ftp://data.pdbj.org/pub/pdb/validation_reports/kv/3kvn	HTTPS FTP

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Related structure data

Similar structure data	4kqo-1 4wek-d 6y6z-d 5df7-1 6r3x-d 6r40-d 4oom-d 6r42-d 4wel-d 6vje-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

X: Esterase estA

A: Esterase estA

hetero molecules

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

1

X: Esterase estA

hetero molecules

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

2

A: Esterase estA

hetero molecules

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

Unit cell

Length a, b, c (Å)	143.826, 143.826, 186.883
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	90
Space group name H-M	P42₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	X
2	1	A

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	ASN	ASN	chain X and (resseq 1:77 or resseq 82:111 or resseq...	X	A	1 - 77	11 - 87
1	2	ILE	ILE	GLU	GLU	chain X and (resseq 1:77 or resseq 82:111 or resseq...	X	A	82 - 111	92 - 121
1	3	LEU	LEU	PRO	PRO	chain X and (resseq 1:77 or resseq 82:111 or resseq...	X	A	132 - 203	142 - 213
1	4	LEU	LEU	GLY	GLY	chain X and (resseq 1:77 or resseq 82:111 or resseq...	X	A	208 - 395	218 - 405
1	5	TYR	TYR	ASP	ASP	chain X and (resseq 1:77 or resseq 82:111 or resseq...	X	A	397 - 475	407 - 485
1	6	HIS	HIS	PHE	PHE	chain X and (resseq 1:77 or resseq 82:111 or resseq...	X	A	485 - 622	495 - 632
2	1	ALA	ALA	ASN	ASN	chain A and (resseq 1:77 or resseq 82:111 or resseq...	A	B	1 - 77	11 - 87
2	2	ILE	ILE	GLU	GLU	chain A and (resseq 1:77 or resseq 82:111 or resseq...	A	B	82 - 111	92 - 121
2	3	LEU	LEU	PRO	PRO	chain A and (resseq 1:77 or resseq 82:111 or resseq...	A	B	132 - 203	142 - 213
2	4	LEU	LEU	GLY	GLY	chain A and (resseq 1:77 or resseq 82:111 or resseq...	A	B	208 - 395	218 - 405
2	5	TYR	TYR	ASP	ASP	chain A and (resseq 1:77 or resseq 82:111 or resseq...	A	B	397 - 475	407 - 485
2	6	HIS	HIS	PHE	PHE	chain A and (resseq 1:77 or resseq 82:111 or resseq...	A	B	485 - 622	495 - 632

#1: Protein	Esterase estA Mass: 68547.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: estA, papA, PA5112 / Production host: Escherichia coli (E. coli) / References: UniProt: O33407, carboxylesterase
#2: Chemical	ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE Mass: 306.438 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₅ / Comment: C8E, detergent*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H₂O
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: 3.52 Å³/Da / Density % sol: 65.1 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 45% PEG400, 0.8 M ammonium formate, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 26, 2009
Radiation	Monochromator: Si-111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 67607 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell	Resolution: 2.5→2.54 Å / % possible all: 99.6

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Processing

Software

Name	Version	Classification
CBASS		data collection
SOLVE		phasing
PHENIX	(phenix.refine)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.499→39.178 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.69 / σ(F): 1.33 / Phase error: 26.37 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.255	1976	2.93 %	RANDOM
R_work	0.204	65418	-	-
obs	0.206	67394	98.53 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 55.347 Å² / k_sol: 0.35 e/Å³

Displacement parameters

B_iso max: 213.45 Å² / B_iso mean: 49.621 Å² / B_iso min: 14.89 Å²

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

Refinement step

Cycle: LAST / Resolution: 2.499→39.178 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9591	0	62	449	10102

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9874
X-RAY DIFFRACTION	f_angle_d	1.09	13399
X-RAY DIFFRACTION	f_dihedral_angle_d	18.324	3475
X-RAY DIFFRACTION	f_chiral_restr	0.067	1389
X-RAY DIFFRACTION	f_plane_restr	0.004	1805

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	X	4437	X-RAY DIFFRACTION	POSITIONAL	0.045
1	2	A	4437	X-RAY DIFFRACTION	POSITIONAL	0.045

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.499-2.5615	0.3122	141	0.2515	4622	X-RAY DIFFRACTION	99
2.5615-2.6307	0.3412	140	0.2414	4647	X-RAY DIFFRACTION	99
2.6307-2.7081	0.2947	140	0.2252	4651	X-RAY DIFFRACTION	99
2.7081-2.7955	0.2939	139	0.224	4607	X-RAY DIFFRACTION	99
2.7955-2.8954	0.2662	141	0.2229	4631	X-RAY DIFFRACTION	99
2.8954-3.0113	0.3195	139	0.235	4645	X-RAY DIFFRACTION	99
3.0113-3.1483	0.2797	141	0.2383	4646	X-RAY DIFFRACTION	99
3.1483-3.3142	0.3102	140	0.2252	4643	X-RAY DIFFRACTION	99
3.3142-3.5217	0.2607	141	0.2097	4672	X-RAY DIFFRACTION	99
3.5217-3.7934	0.2457	142	0.1958	4676	X-RAY DIFFRACTION	99
3.7934-4.1748	0.2396	139	0.1858	4664	X-RAY DIFFRACTION	98
4.1748-4.778	0.2274	140	0.1715	4695	X-RAY DIFFRACTION	98
4.778-6.0162	0.2071	143	0.1726	4744	X-RAY DIFFRACTION	98
6.0162-39.1832	0.1862	150	0.1719	4875	X-RAY DIFFRACTION	96

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	0.3411	-0.3247	-0.1809	0.4635	0.1174	0.8106	0.0785	-0.0461	-0.0435	0.092	-0.0231	0.018	0.5618	-0.751	-0.0459	0.3703	-0.1861	-0.0255	0.5823	-0.0049	0.1065	-11.1203	40.0153	78.0506
2	0.4951	-0.3729	-0.4519	0.1196	-0.2677	0.1589	-0.1434	0.1985	-0.1866	0.1053	0.0741	0.1114	1.6894	-1.5521	0.0086	0.6873	-0.5773	-0.0412	0.861	-0.0014	0.1399	-15.832	28.2255	78.0351
3	1.5214	-0.2	0.3013	0.185	0.3642	0.6714	0.1384	-0.2638	-0.4459	-0.0272	0.0683	-0.0504	0.9541	-0.4238	-0.1329	0.6948	-0.1375	-0.097	0.3799	-0.0164	0.2083	1.6798	23.6689	78.5476
4	0.1614	-0.1065	0.049	0.5671	0.0029	2.2519	0.0365	0.2358	0.0049	-0.19	0.0344	-0.1291	0.2836	-0.0182	-0.0655	0.3368	-0.0608	0.0201	0.4743	-0.0054	0.1316	3.802	42.4223	59.9413
5	0.3023	-0.1203	-0.4554	0.7119	-0.3357	2.0303	0.0231	0.2716	0.0323	-0.3205	0.0083	-0.0984	0.3614	0.168	-0.0438	0.5731	-0.0692	0.0687	0.621	-0.0204	0.1241	-1.5412	40.0415	30.4733
6	-0.212	-0.1195	0.2876	-0.1876	0.3987	1.3625	0.0148	0.0074	-0.0117	-0.2928	0.0292	0.0276	0.2823	-0.4768	-0.015	0.5837	-0.095	-0.0016	0.7448	0.0083	0.1464	-6.1909	43.1373	33.1396
7	0.4936	-0.2771	0.4408	0.9212	-0.377	0.5589	-0.0365	0.0196	0.0246	-0.0141	-0.0227	-0.1061	-0.4337	0.2141	0.0448	0.5143	0.0154	0.0446	0.3588	0.0318	0.1275	49.9465	30.748	74.1474
8	1.0153	-0.4183	-0.2244	0.3348	0.3784	-1.49	-0.186	0.0339	0.1103	0.1041	0.0548	-0.0876	-0.554	0.0405	0.1087	0.7535	0.1564	0.0011	0.2424	0.05	0.1603	40.471	39.1397	74.1839
9	0.2237	0.8371	0.5031	1.0317	-0.1842	-0.2235	0.1578	0.0249	0.0416	0.1363	-0.0173	0.3406	-0.5582	-0.8329	-0.0931	0.3619	0.1359	0.0411	0.4798	0.0539	0.1467	30.3379	24.8578	77.9295
10	0.554	-0.0748	-0.4165	0.2941	-0.0454	1.9755	0.0295	0.2335	-0.0487	-0.2999	-0.077	0.0082	0.2182	-0.1112	0.0572	0.4918	0.0301	0.0089	0.2951	-0.0064	0.109	45.059	13.3422	59.3264
11	0.8799	0.1004	-0.6922	0.4283	0.6985	1.6621	0.0336	0.422	-0.0887	-0.3148	-0.0691	0.0326	0.3067	-0.4461	0.0392	0.7148	0.0689	-0.0335	0.6233	-0.0661	0.1067	41.3545	14.575	29.5756
12	0.4886	0.2383	0.4681	-0.2806	-0.2449	-0.1136	0.1536	0.4169	-0.092	-0.2333	-0.1832	0.0527	-0.0234	-0.1044	-0.0294	0.8425	0.1464	0.0273	0.6756	0.0008	0.166	46.3405	17.9911	30.6748

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid -4:108)	A	-4 - 108
2	X-RAY DIFFRACTION	2	(chain A and resid 109:141)	A	109 - 141
3	X-RAY DIFFRACTION	3	(chain A and resid 142:180)	A	142 - 180
4	X-RAY DIFFRACTION	4	(chain A and resid 181:375)	A	181 - 375
5	X-RAY DIFFRACTION	5	(chain A and resid 376:537)	A	376 - 537
6	X-RAY DIFFRACTION	6	(chain A and resid 538:622)	A	538 - 622
7	X-RAY DIFFRACTION	7	(chain X and resid -5:108)	X	-5 - 108
8	X-RAY DIFFRACTION	8	(chain X and resid 109:141)	X	109 - 141
9	X-RAY DIFFRACTION	9	(chain X and resid 142:180)	X	142 - 180
10	X-RAY DIFFRACTION	10	(chain X and resid 181:375)	X	181 - 375
11	X-RAY DIFFRACTION	11	(chain X and resid 376:536)	X	376 - 536
12	X-RAY DIFFRACTION	12	(chain X and resid 537:622)	X	537 - 622

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