4K7Q | pdb_00004k7q

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 PDBTM MemProtMD mpstruc

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.304 (Depositor), 0.304 (DCC)
R-Value Work:
0.251 (Depositor), 0.253 (DCC)
R-Value Observed:
0.255 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1007/s10969-013-9154-x
Primary Citation 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.

Organizational Affiliation

Los Alamos National Laboratory, Los Alamos, NM 87545, USA. lwhung@lanl.gov

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31224
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZLD Query on ZLD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.304 (Depositor), 0.304 (DCC)
R-Value Work: 0.251 (Depositor), 0.253 (DCC)
R-Value Observed: 0.255 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2013-07-03

Deposition Author(s):

Revision History (Full details and data files)

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