6ZRE | pdb_00006zre

Deciphering the role of the channel constrictions in the opening mechanism of MexAB-OprM efflux pump from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb6ZRE/pdb

• Classification: TRANSLOCASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2020-07-13 Released: 2021-07-28 
• Deposition Author(s): Ntsogo Enguene, Y.V., Monlezun, L., Ma, M., Garnier, C., Lascombe, M.B., Salem, M., Guenard, S., Plesiat, P., Llanes, C., Phan, G., Broutin, I.
• Funding Organization(s): French National Research Agency

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.318 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.293 (Depositor), 0.290 (DCC) 

Starting Model: experimental

Literature

Deciphering the role of OprM constrictions in the opening mechanism of the MexAB-OprM efflux pump from Pseudomonas aeruginosa.

Ntsogo Enguene, Y.V., Monlezun, L., Ma, M., Garnier, C., Lascombe, M.B., Salem, M., Guenard, S., Plesiat, P., Llanes, C., Phan, G., Broutin, I.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 106.66 kDa 
• Atom Count: 7,204 
• Modeled Residue Count: 912 
• Deposited Residue Count: 948 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein OprM	A, B	474	Pseudomonas aeruginosa PAO1	Mutation(s): 4  Gene Names: oprM, oprK, PA0427 Membrane Entity: Yes
UniProt
Find proteins for Q51487 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q51487  Go to UniProtKB:  Q51487

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PLM (Subject of Investigation/LOI)	C [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
SO4 (Subject of Investigation/LOI)	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.318 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.293 (Depositor), 0.290 (DCC) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.797	α = 90
b = 86.797	β = 90
c = 1046.53	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-28 
Deposition Author(s): Ntsogo Enguene, Y.V., Monlezun, L., Ma, M., Garnier, C., Lascombe, M.B., Salem, M., Guenard, S., Plesiat, P., Llanes, C., Phan, G., Broutin, I.

---

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-12-BSV8-0010-01

Revision History  

• Version 1.0: 2021-07-28
  Type: Initial release
  
• Version 2.0: 2022-07-20
  Type: Coordinate replacement
  Reason: Real space R-factor
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary