PDB-5azs: Crystal structure of a membrane protein from Pseudomonas aeruginosa

ID or keywords:

Entry

Database: PDB / ID: 5azs

Title

Crystal structure of a membrane protein from Pseudomonas aeruginosa

Components

Outer membrane protein OprJ

Keywords

MEMBRANE PROTEIN / Alpha barrel / Beta barrel

Function / homology

Function and homology information

response to xenobiotic stimulus => GO:0009410 / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / cell outer membrane / membrane => GO:0016020 / response to antibiotic
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Yonehara, R. / Yamashita, E. / Nakagawa, A.

Citation

Journal: Proteins / Year: 2016
Title: Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of Pseudomonas aeruginosa.
Authors: Yonehara, R. / Yamashita, E. / Nakagawa, A.

History

Deposition	Oct 21, 2015	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 8, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 26, 2020	Group: Data collection / Database references / Derived calculations Category: citation / diffrn_source / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_initial_refinement_model Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5azs.cif.gz	501.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5azs.ent.gz	423.5 KB	Display	PDB format
PDBx/mmJSON format	5azs.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5azs_validation.pdf.gz	450.4 KB	Display	wwPDB validaton report
Full document	5azs_full_validation.pdf.gz	459.9 KB	Display
Data in XML	5azs_validation.xml.gz	42.2 KB	Display
Data in CIF	5azs_validation.cif.gz	58 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/az/5azs ftp://data.pdbj.org/pub/pdb/validation_reports/az/5azs	HTTPS FTP

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Related structure data

Related structure data	5azoC 5azpC 1wp1S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1wp1-1 3pik-1 4k7r-1 4y1k-1 5nsw-d 1yc9-1 3d5k-d 5azo-1 2xmn-d 4y1k-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	#95 - Nov 2007 Multidrug Resistance Transporters similarity (3) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1)

Deposited unit

A: Outer membrane protein OprJ

B: Outer membrane protein OprJ

C: Outer membrane protein OprJ

153 kDa, 3 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)	86.329, 92.388, 252.765
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Outer membrane protein OprJ Mass: 51080.039 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: oprJ, PA4597 / Production host: Escherichia coli (E. coli) / References: UniProt: Q51397

#1: Protein

Outer membrane protein OprJ

Mass: 51080.039 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: oprJ, PA4597 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q51397

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.29 Å³/Da / Density % sol: 62.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 4000, sodium acetate, sodium formate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 12, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 3.1→50 Å / Num. obs: 36834 / % possible obs: 97.2 % / Redundancy: 4.5 % / Net I/σ(I): 20.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0131	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1WP1

1wp1

Resolution: 3.1→50 Å / Cor.coef. F_o:F_c: 0.907 / Cor.coef. F_o:F_c free: 0.887 / SU B: 80.891 / SU ML: 0.561 / Cross valid method: THROUGHOUT / ESU R Free: 0.528 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30744	1807	4.9 %	RANDOM
R_work	0.26861	-	-	-
obs	0.27051	34702	97.17 %	-

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: 113.175 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	10.78 Å²	-0 Å²	0 Å²
2-	-	-5.69 Å²	-0 Å²
3-	-	-	-5.09 Å²

Refinement step

Cycle: 1 / Resolution: 3.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10096	0	0	0	10096

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	10240
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9880
X-RAY DIFFRACTION	r_angle_refined_deg	1.124	1.967	13854
X-RAY DIFFRACTION	r_angle_other_deg	0.908	3	22506
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.479	5	1305
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.074	22.701	511
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.867	15	1704
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.218	15	139
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	1553
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	11935
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2486
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	1.522	7.875	5238
X-RAY DIFFRACTION	r_mcbond_other	1.521	7.875	5237
X-RAY DIFFRACTION	r_mcangle_it	2.654	11.815	6537
X-RAY DIFFRACTION	r_mcangle_other	2.654	11.816	6538
X-RAY DIFFRACTION	r_scbond_it	1.411	8.054	5002
X-RAY DIFFRACTION	r_scbond_other	1.411	8.055	5003
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.534	12.003	7318
X-RAY DIFFRACTION	r_long_range_B_refined	4.508	61.175	11392
X-RAY DIFFRACTION	r_long_range_B_other	4.508	61.178	11393
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.1→3.18 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.452	135	-
R_work	0.422	2467	-
obs	-	-	95.56 %

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	0.2399	-0.1378	-0.191	0.4272	0.4207	0.5963	0.1171	0.0099	0.0121	-0.1514	-0.1698	0.1023	-0.5529	-0.2283	0.0528	1.0029	0.1696	0.0253	0.1874	-0.007	0.0499	-56.9451	9.1523	34.1475
2	0.7187	-0.2479	-0.5767	0.6672	-0.6609	2.7325	-0.4835	0.163	0.0253	0.1587	-0.1221	-0.2421	-0.1586	-0.5624	0.6056	1.2239	0.1843	-0.0157	0.3121	-0.1184	0.2183	-55.2276	12.2357	35.4882
3	1.5152	-0.9402	-2.9731	1.4435	2.0396	7.7562	0.0894	0.1068	-0.11	-0.3015	-0.0858	0.2385	-0.2691	-0.3827	-0.0036	0.6315	0.1699	-0.1032	0.2234	0.0061	0.0827	-48.6448	-1.0815	-21.6372
4	1.006	-1.9102	1.0823	3.7372	-2.1937	1.3475	-0.2573	0.0749	0.0509	0.6397	0.1535	-0.1456	-0.5259	-0.31	0.1038	0.9024	0.4909	-0.0662	0.8402	-0.0963	0.0613	-59.9236	11.9715	-3.1216
5	0.3402	-0.0887	-0.0999	0.1897	-0.0598	1.431	0.0482	-0.0586	0.1175	-0.0639	-0.0214	-0.0519	-0.4666	0.0767	-0.0268	1.018	0.0062	0.0527	0.0197	-0.0151	0.0443	-44.0295	12.4321	21.0646
6	1.6311	-1.3005	-2.9351	3.7551	7.3984	15.2201	-0.2173	0.0069	-0.1769	0.0107	-0.3167	0.2512	-0.036	-0.2575	0.534	0.5415	0.0538	0.021	0.3025	0.0501	0.1541	-43.923	13.7911	-5.9993
7	0.2807	-0.0632	-0.2004	0.2234	0.1495	0.9826	0.0248	-0.1621	-0.0312	-0.0021	0.0273	-0.125	-0.3257	0.2582	-0.0521	0.7337	-0.0973	0.0344	0.1608	0.0128	0.0906	-30.9079	1.7158	29.7287
8	0.3802	0.0217	-0.6124	0.4899	1.5838	6.4628	0.2373	-0.0617	0.1439	-0.1628	-0.0139	-0.0005	-0.6954	0.0433	-0.2234	0.8945	-0.117	0.1392	0.0485	0.0013	0.0902	-25.8835	15.5861	-5.5486
9	0.2933	-0.0291	-0.8135	0.4118	0.3955	2.6636	-0.005	-0.1857	-0.0379	-0.0417	0.0305	-0.0636	-0.1534	0.359	-0.0255	0.6864	-0.0214	0.0129	0.3381	0.1011	0.0607	-29.8685	-11.8144	35.2307
10	0.2624	-0.5706	-0.1673	2.3134	2.0492	3.9472	0.0213	-0.083	-0.0936	0.2013	0.1644	0.1345	0.1083	0.0633	-0.1857	0.5819	-0.0572	0.009	0.2676	0.0474	0.0553	-48.0374	-9.2957	60.9749
11	0.4632	-0.1567	-0.1552	0.3177	0.6351	1.4752	0.0028	-0.0335	0.0213	-0.0968	0.0315	-0.0246	-0.4543	0.2114	-0.0342	0.9173	-0.1318	0.1014	0.1798	0.0426	0.047	-22.3709	-2.7333	-7.0086
12	0.2796	-0.8196	-1.5543	6.6121	-2.7112	21.679	0.0807	0.0045	-0.0073	0.0677	0.0108	-0.1295	-1.136	0.0084	-0.0915	0.3201	-0.1645	0.0727	0.3109	-0.0673	0.3342	-20.0005	-3.8998	9.1526
13	0.0324	-0.0279	-0.0613	0.3062	0.0135	1.0881	0.0535	-0.0367	-0.0499	-0.0528	-0.081	0.0767	-0.1479	-0.1507	0.0275	0.6337	-0.0075	-0.0054	0.3301	0.0115	0.1098	-55.405	-15.6448	35.6342
14	5.2636	1.0218	-6.5598	0.2722	-1.2228	8.6149	-0.04	0.1851	0.0386	-0.0872	0.0276	0.022	0.1546	-0.2476	0.0124	0.413	-0.0005	-0.0048	0.1929	0.0072	0.2491	-30.4286	-16.9242	-9.2769
15	2.0048	0.4654	-1.9635	0.1719	-0.4543	1.9476	0.0195	-0.0244	-0.092	-0.1483	-0.0783	-0.0522	-0.0531	0.0657	0.0588	0.8304	0.0386	0.0284	0.1632	0.0016	0.058	-31.2159	-16.2592	-6.4322
16	1.4825	-1.1091	-3.1555	1.0049	1.8644	8.2335	0.0604	0.0403	-0.0208	-0.1297	0.0711	0.0386	-0.0095	-0.4364	-0.1315	0.3518	0.0548	-0.0266	0.3037	0.0321	0.2142	-64.412	-8.1799	26.3914
17	0.2388	0.0435	-0.3466	0.2888	0.0898	2.3509	-0.1064	0.0365	-0.0625	-0.0916	-0.117	0.0903	0.0844	-0.4988	0.2233	0.6886	0.1176	-0.003	0.2338	-0.0303	0.078	-58.1415	-8.3426	28.2935
18	0.4493	0.0443	0.109	0.5548	0.6583	0.7929	0.1174	0.1471	0.055	-0.1695	-0.1261	0.0143	-0.1813	-0.1382	0.0087	0.9783	0.0964	0.0412	0.1503	0.0448	0.0195	-38.9153	-13.4656	-12.5789

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 108
2	X-RAY DIFFRACTION	2	A	109 - 160
3	X-RAY DIFFRACTION	3	A	161 - 231
4	X-RAY DIFFRACTION	4	A	232 - 254
5	X-RAY DIFFRACTION	5	A	255 - 415
6	X-RAY DIFFRACTION	6	A	416 - 443
7	X-RAY DIFFRACTION	7	B	1 - 192
8	X-RAY DIFFRACTION	8	B	193 - 250
9	X-RAY DIFFRACTION	9	B	251 - 305
10	X-RAY DIFFRACTION	10	B	306 - 345
11	X-RAY DIFFRACTION	11	B	346 - 429
12	X-RAY DIFFRACTION	12	B	430 - 443
13	X-RAY DIFFRACTION	13	C	1 - 145
14	X-RAY DIFFRACTION	14	C	146 - 191
15	X-RAY DIFFRACTION	15	C	192 - 263
16	X-RAY DIFFRACTION	16	C	264 - 295
17	X-RAY DIFFRACTION	17	C	296 - 391
18	X-RAY DIFFRACTION	18	C	392 - 455

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