5AZP

Crystal structure of a membrane protein from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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Ligand Structure Quality Assessment 


This is version 1.2 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

  • DOI: 10.1002/prot.25022
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Multidrug efflux outer membrane protein OprNA, B, C455Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: oprNPA2495
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I0Y7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
3PK
Query on 3PK

Download Ideal Coordinates CCD File 
D [auth A],
LA [auth C]
(2S)-1-(pentanoyloxy)propan-2-yl hexanoate
C14 H26 O4
XIGVTLHUQMMWJT-LBPRGKRZSA-N
 Ligand Interaction
OYA
Query on OYA

Download Ideal Coordinates CCD File 
E [auth A],
MA [auth C]
OCTANAL
C8 H16 O
NUJGJRNETVAIRJ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
AB [auth C],
HA [auth B],
S [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 257.515α = 90
b = 257.515β = 90
c = 81.825γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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