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

ID or keywords:

Entry

Database: PDB / ID: 5azp

Title

Crystal structure of a membrane protein from Pseudomonas aeruginosa

Components

Multidrug efflux outer membrane protein OprN

Keywords

MEMBRANE PROTEIN / Alpha barrel / Beta barrel

Function / homology

Function and homology information

efflux transmembrane transporter activity / transmembrane transporter activity / cell outer membrane / transmembrane transport / membrane
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.69 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	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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 Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: audit_author / chem_comp ...audit_author / chem_comp / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_initial_refinement_model Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms ..._audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5azp.cif.gz	576.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5azp.ent.gz	473.4 KB	Display	PDB format
PDBx/mmJSON format	5azp.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5azp_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	5azp_full_validation.pdf.gz	2.3 MB	Display
Data in XML	5azp_validation.xml.gz	75 KB	Display
Data in CIF	5azp_validation.cif.gz	113.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/az/5azp ftp://data.pdbj.org/pub/pdb/validation_reports/az/5azp	HTTPS FTP

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Related structure data

Related structure data	5azoSC 5azsC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5iuy-d 5azo-1 4mt0-1 4y1k-1 3d5k-d 5nsw-d 4y1k-2 6q7j-d 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 (2)

Deposited unit

A: Multidrug efflux outer membrane protein OprN

B: Multidrug efflux outer membrane protein OprN

C: Multidrug efflux outer membrane protein OprN

hetero molecules

155 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)	257.515, 257.515, 81.825
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

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Protein / Sugars , 2 types, 11 molecules ABC

#1: Protein

Multidrug efflux outer membrane protein OprN

Mass: 49686.188 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 26-472
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: oprN, PA2495 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q9I0Y7

#4: Sugar

ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside

Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C₁₄H₂₈O₆ / Comment: detergent*YM

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Non-polymers , 7 types, 1931 molecules

#2: Chemical	ChemComp-3PK / (2S)-1-(pentanoyloxy)propan-2-yl hexanoate Mass: 258.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₆O₄
#3: Chemical	ChemComp-OYA / OCTANAL / OCTYL ALDEHYDE Mass: 128.212 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₆O
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: CH₂O₂
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₃O₂
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1885 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 4.55 Å³/Da / Density % sol: 72.97 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / 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 23, 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: 1.69→50 Å / Num. obs: 297648 / % possible obs: 99.5 % / Redundancy: 3.6 % / Net I/σ(I): 22.9

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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: 5AZO

5azo

Resolution: 1.69→50 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.961 / SU B: 2.816 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17974	15033	5.1 %	RANDOM
R_work	0.16008	-	-	-
obs	0.16109	282614	99.4 %	-

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: 26.502 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.05 Å²	0 Å²	0 Å²
2-	-	-0.05 Å²	0 Å²
3-	-	-	0.11 Å²

Refinement step

Cycle: 1 / Resolution: 1.69→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10290	0	379	1885	12554

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	11372
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	11063
X-RAY DIFFRACTION	r_angle_refined_deg	1.973	1.989	15437
X-RAY DIFFRACTION	r_angle_other_deg	1.097	2.992	25414
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.04	5	1521
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.095	22.662	571
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.465	15	1909
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.251	15	167
X-RAY DIFFRACTION	r_chiral_restr	0.125	0.2	1740
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	13208
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2715
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	1.523	1.737	5562
X-RAY DIFFRACTION	r_mcbond_other	1.494	1.733	5554
X-RAY DIFFRACTION	r_mcangle_it	2.155	2.587	6986
X-RAY DIFFRACTION	r_mcangle_other	2.155	2.588	6987
X-RAY DIFFRACTION	r_scbond_it	3.08	2.327	5810
X-RAY DIFFRACTION	r_scbond_other	3.079	2.327	5811
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.644	3.29	8359
X-RAY DIFFRACTION	r_long_range_B_refined	9.009	18.087	15352
X-RAY DIFFRACTION	r_long_range_B_other	9.01	18.089	15353
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.689→1.733 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.272	988	-
R_work	0.257	20855	-
obs	-	-	98.81 %

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	0.3259	-0.0219	0.0787	0.0419	-0.0908	0.2224	-0.048	-0.1197	0.0924	0.0322	-0.0268	-0.0499	-0.0317	0.0327	0.0747	0.0948	0.027	-0.0874	0.0679	-0.0309	0.1033	-70.2873	-20.2725	-31.3174
2	0.0255	0.0035	-0.0326	0.1998	0.0063	0.0531	-0.0064	-0.0168	-0.015	0.025	-0.0173	-0.0114	0.0172	0.0127	0.0237	0.0647	0.0255	0.0075	0.0317	0.0146	0.0451	-85.979	-44.0509	-41.1828
3	0.0336	0.0774	-0.0625	0.3501	-0.1084	0.1421	-0.0045	0.0084	0.0059	-0.0004	0.0174	0.0724	-0.0093	-0.0402	-0.0129	0.0544	0.0275	-0.003	0.0396	0.0121	0.0405	-105.2742	4.2295	-47.2506
4	0.0441	-0.0201	-0.0285	0.014	0.0154	0.051	-0.016	-0.0313	-0.006	0.0163	0.0168	-0.0108	0.0141	0.0324	-0.0008	0.0609	0.0361	-0.0004	0.0383	0.0107	0.0505	-73.1731	-40.7746	-41.7891
5	0.4281	-0.228	-0.2213	1.0952	-0.2655	0.2656	0.0059	-0.0305	0.0102	-0.0007	0.04	0.0759	-0.0115	0.0027	-0.0458	0.0729	0.0236	-0.0033	0.021	-0.0025	0.0237	-96.6435	21.544	-44.4474
6	0.3145	-0.4002	0.2021	1.08	-0.3466	0.1458	0.0097	-0.0144	-0.0109	0.0149	-0.0109	0.0113	-0.0071	-0.0034	0.0013	0.0628	0.0193	-0.0018	0.0342	0.0102	0.0308	-90.0765	-4.5572	-38.0814
7	0.2145	-0.4208	0.1914	1.6589	-0.75	0.4685	-0.0627	-0.0071	-0.0619	0.0708	0.137	0.2134	-0.006	-0.1256	-0.0743	0.0247	-0.0179	0.0144	0.0497	0.0063	0.0889	-112.9496	-26.6315	-57.8709
8	0.0167	-0.022	-0.0384	0.0412	0.0673	0.1191	-0.0228	0.0061	-0.0008	0.0322	0.0077	0.0006	0.0443	-0.0043	0.015	0.0759	0.0062	0.006	0.0243	-0.0044	0.0492	-89.7658	-45.8154	-67.697
9	0.0196	0.0181	0.0377	0.1519	0.0982	0.1282	-0.0233	0.0192	-0.0008	-0.0493	0.0213	-0.0163	-0.0479	0.0281	0.002	0.0804	-0.0129	-0.0076	0.0348	0.0022	0.0365	-89.0971	7.3394	-73.4171
10	2.4207	-1.1136	0.8008	3.1309	-2.3316	1.7368	-0.2244	0.0421	0.1214	0.0517	0.1914	-0.0443	-0.0355	-0.1433	0.033	0.029	0.0098	-0.0139	0.0718	-0.0055	0.0214	-113.389	-19.4432	-63.8973
11	0.0197	0.0173	-0.0161	0.1349	0.0013	0.0445	-0.0381	-0.0033	-0.0084	-0.0084	0.0261	0.0069	0.0251	-0.006	0.012	0.0779	0.0152	0.018	0.0145	0.0053	0.0392	-95.5113	-45.3617	-55.6648
12	0.027	0.0705	0.0248	0.8942	0.1112	0.0385	-0.0281	0.01	-0.0021	-0.0457	0.0158	0.0189	-0.0302	0.001	0.0123	0.0744	0.0018	-0.0162	0.0283	0.0058	0.0348	-100.5348	6.5745	-66.2911
13	0.0171	-0.2354	0.0384	7.1393	-0.5928	0.0895	0.0123	0.0244	-0.003	-0.136	-0.0055	0.0099	0.0164	0.0502	-0.0068	0.0837	0.0206	0.0277	0.0638	-0.003	0.0255	-71.974	-27.9901	-80.9817
14	0.0723	-0.2176	0.0145	0.6601	-0.0299	0.0533	0.0138	0.0024	0.0134	-0.0443	0.0058	-0.0507	0.0283	0.0615	-0.0195	0.046	0.0301	0.0112	0.076	-0.0157	0.0501	-62.3977	-25.2343	-60.3904
15	0.1496	-0.0963	-0.0078	0.0697	-0.014	0.0495	0.005	-0.0092	-0.0295	-0.014	-0.0054	0.0245	0.0367	0.0428	0.0004	0.1114	0.0505	-0.0253	0.0413	-0.0087	0.0462	-69.066	-58.4343	-59.2304
16	0.0245	0.0071	0.0159	0.1589	0.018	0.0246	-0.0214	-0.0145	-0.006	0.0125	0.0334	-0.0334	-0.0219	0.013	-0.0119	0.0561	0.0042	0.0055	0.0455	-0.011	0.0407	-73.881	6.9633	-49.1015
17	0.0066	-0.0056	-0.0079	0.0091	0.0233	0.0943	0.0105	0.0026	-0.0008	-0.0026	0.0007	0.0068	0.0297	0.0333	-0.0112	0.0629	0.021	-0.0057	0.0199	-0.0071	0.0531	-73.2209	-40.2155	-69.1725
18	0.3056	-0.5365	-0.0597	1.0223	0.2126	0.1734	-0.0463	-0.0085	0.0291	0.0389	0.039	-0.0585	-0.0331	0.034	0.0073	0.0705	-0.0001	0.0053	0.016	-0.0088	0.0404	-77.335	14.0046	-59.0633

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 27
2	X-RAY DIFFRACTION	2	A	28 - 155
3	X-RAY DIFFRACTION	3	A	156 - 251
4	X-RAY DIFFRACTION	4	A	252 - 373
5	X-RAY DIFFRACTION	5	A	374 - 412
6	X-RAY DIFFRACTION	6	A	413 - 446
7	X-RAY DIFFRACTION	7	B	1 - 31
8	X-RAY DIFFRACTION	8	B	32 - 155
9	X-RAY DIFFRACTION	9	B	156 - 250
10	X-RAY DIFFRACTION	10	B	251 - 263
11	X-RAY DIFFRACTION	11	B	264 - 378
12	X-RAY DIFFRACTION	12	B	379 - 450
13	X-RAY DIFFRACTION	13	C	1 - 20
14	X-RAY DIFFRACTION	14	C	21 - 89
15	X-RAY DIFFRACTION	15	C	90 - 146
16	X-RAY DIFFRACTION	16	C	147 - 259
17	X-RAY DIFFRACTION	17	C	260 - 378
18	X-RAY DIFFRACTION	18	C	379 - 444

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Protein / Sugars , 2 types, 11 molecules ABC

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Non-polymers , 7 types, 1931 molecules

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