4K7Q

Crystal Structure of AcrB Complexed with Linezolid at 3.5 Resolution

• PDB DOI: https://doi.org/10.2210/pdb4K7Q/pdb

• Classification: MEMBRANE PROTEIN/ANTIBIOTIC
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2013-04-17 Released: 2013-07-03 
• Deposition Author(s): Hung, L.W., Kim, H.B., Murakami, S., Gupta, G., Kim, C.Y., Terwilliger, T.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.304 
• R-Value Work: 0.251 
• R-Value Observed: 0.255 

Literature

Crystal structure of AcrB complexed with linezolid at 3.5 Angstrom resolution.

Hung, L.W., Kim, H.B., Murakami, S., Gupta, G., Kim, C.Y., Terwilliger, T.C.

(2013) J Struct Funct Genomics 14: 71-75

• PubMed: 23673416 
• DOI: https://doi.org/10.1007/s10969-013-9154-x
• Primary Citation of Related Structures:  
  4K7Q


• PubMed Abstract: 
  

  AcrB is an inner membrane resistance-nodulation-cell division efflux pump and is part of the AcrAB-TolC tripartite efflux system. We have determined the crystal structure of AcrB with bound Linezolid at a resolution of 3.5 Å. The structure shows that Linezolid binds to the A385/F386 loops of the symmetric trimer of AcrB. A conformational change of a loop in the bottom of the periplasmic cleft is also observed.

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Organizational Affiliation: 

Los Alamos National Laboratory, Los Alamos, NM 87545, USA. [e-mail]

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)

Macromolecule Content

• Total Structure Weight: 114.56 kDa 
• Atom Count: 7,700 
• Modelled Residue Count: 1,011 
• Deposited Residue Count: 1,053 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acriflavine resistance protein B	A	1,053	Escherichia coli K-12	Mutation(s): 0  Gene Names: acrB, acrE, b0462, JW0451 Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224  Go to UniProtKB:  P31224

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZLD	B [auth A]	N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide C16 H20 F N3 O4 TYZROVQLWOKYKF-ZDUSSCGKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.304 
• R-Value Work: 0.251 
• R-Value Observed: 0.255 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.685	α = 90
b = 144.685	β = 90
c = 519.357	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Hung, L.W., Kim, H.B., Murakami, S., Gupta, G., Kim, C.Y., Terwilliger, T.C.

Revision History  

• Version 1.0: 2013-07-03
  Type: Initial release
  
• Version 1.1: 2015-07-22
  Changes: Non-polymer description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations