5AZP | pdb_00005azp

Crystal structure of a membrane protein from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb5AZP/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2015-10-21 Released: 2016-06-08
Deposition Author(s): Yonehara, R., Yamashita, E., Nakagawa, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.180 (Depositor), 0.191 (DCC)
R-Value Work:
0.160 (Depositor), 0.173 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of Pseudomonas aeruginosa.

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

(2016) Proteins 84: 759-769

PubMed: 26914226 Search on PubMed
DOI: https://doi.org/10.1002/prot.25022
Primary Citation Related Structures:
5AZO, 5AZP, 5AZS

PubMed Abstract:
The genome of Pseudomonas aeruginosa encodes tripartite efflux pumps that extrude functionally and structurally dissimilar antibiotics from the bacterial cell. MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY-OprM are the main tripartite efflux pumps responsible for multidrug resistance in P. aeruginosa. The outer membrane factors OprN, OprJ, and OprM are essential components of functional tripartite efflux pumps. To elucidate the structural basis of multidrug resistance, we determined the crystal structures of OprN and OprJ. These structures revealed several features, including tri-acylation of the N-terminal cysteine, a small pore in the β-barrel domain, and a tightly sealed gate in the α-barrel domain. Despite the overall similarity of OprN, OprJ, and OprM, a comparison of their structures and electrostatic distributions revealed subtle differences at the periplasmic end of the α-barrel domain. These results suggested that the overall structures of these outer membrane factors are specifically optimized for particular tripartite efflux pumps. Proteins 2016; 84:759-769. © 2016 Wiley Periodicals, Inc.

Organizational Affiliation

Institute for Protein Research, Osaka University, Suita, Japan.

Macromolecule Content

Total Structure Weight: 154.7 kDa
Atom Count: 13,057
Modeled Residue Count: 1,340
Deposited Residue Count: 1,365
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux outer membrane protein OprN	A, B, C	455	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: oprN, PA2495 Membrane Entity: Yes
UniProt
Find proteins for Q9I0Y7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I0Y7 Go to UniProtKB: Q9I0Y7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I0Y7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain V [auth B] SDF format, chain NA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain NA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain NA [auth C]	F [auth A] G [auth A] H [auth A] NA [auth C] OA [auth C] F [auth A], G [auth A], H [auth A], NA [auth C], OA [auth C], PA [auth C], QA [auth C], V [auth B]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain V [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain V [auth B]
3PK Query on 3PK Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain LA [auth C] MOL2 format, chain D [auth A] MOL2 format, chain LA [auth C] mmCIF format, chain D [auth A] mmCIF format, chain LA [auth C]	D [auth A], LA [auth C]	(2S)-1-(pentanoyloxy)propan-2-yl hexanoate C₁₄ H₂₆ O₄ XIGVTLHUQMMWJT-LBPRGKRZSA-N		Interactions Focus chain D [auth A] Focus chain LA [auth C] Interactions & Density Focus chain D [auth A] Focus chain LA [auth C]
OYA Query on OYA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain MA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain MA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain MA [auth C]	E [auth A], MA [auth C]	OCTANAL C₈ H₁₆ O NUJGJRNETVAIRJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain MA [auth C] Interactions & Density Focus chain E [auth A] Focus chain MA [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain X [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth B]	I [auth A] J [auth A] K [auth A] L [auth A] RA [auth C] I [auth A], J [auth A], K [auth A], L [auth A], RA [auth C], SA [auth C], TA [auth C], UA [auth C], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A]	BB [auth C] CB [auth C] DB [auth C] EB [auth C] IA [auth B] BB [auth C], CB [auth C], DB [auth C], EB [auth C], IA [auth B], JA [auth B], KA [auth B], T [auth A], U [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain T [auth A] Focus chain U [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain GA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] SDF format, chain P [auth A] SDF format, chain FA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain FA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain FA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain S [auth A] SDF format, chain HA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain S [auth A] MOL2 format, chain HA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain S [auth A] mmCIF format, chain HA [auth B]	AB [auth C], HA [auth B], S [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain HA [auth B] Focus chain S [auth A] Interactions & Density Focus chain AB [auth C] Focus chain HA [auth B] Focus chain S [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.180 (Depositor), 0.191 (DCC)
R-Value Work: 0.160 (Depositor), 0.173 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 257.515	α = 90
b = 257.515	β = 90
c = 81.825	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-06-08

Deposition Author(s):

Yonehara, R.

Yamashita, E.

Nakagawa, A.

Revision History (Full details and data files)

Version 1.0: 2016-06-08
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2024-11-13
Changes: Structure summary