2W1B | pdb_00002w1b

The structure of the efflux pump AcrB in complex with bile acid

PDB DOI: https://doi.org/10.2210/pdb2W1B/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2008-10-17 Released: 2008-12-09
Deposition Author(s): Drew, D., Klepsch, M.M., Newstead, S., Flaig, R., De Gier, J.W., Iwata, S., Beis, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.85 Å
R-Value Free:
0.349 (Depositor), 0.330 (DCC)
R-Value Work:
0.278 (Depositor), 0.270 (DCC)
R-Value Observed:
0.281 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

The Structure of the Efflux Pump Acrb in Complex with Bile Acid.

Drew, D., Klepsch, M.M., Newstead, S., Flaig, R., De Gier, J.W., Iwata, S., Beis, K.

(2008) Mol Membr Biol 25: 677

PubMed: 19023693 Search on PubMed
DOI: https://doi.org/10.1080/09687680802552257
Primary Citation of Related Structures:
2W1B

PubMed Abstract:
Gastrointestinal bacteria, like Escherichia coli, must remove bile acid to survive in the gut. Bile acid removal in E. coli is thought to be mediated primarily by the multidrug efflux pump, AcrB. Here, we present the structure of E. coli AcrB in complex with deoxycholate at 3.85 A resolution. All evidence suggests that bile acid is transported out of the cell via the periplasmic vestibule of the AcrAB-TolC complex.

Organizational Affiliation

Division of Molecular Biosciences, Membrane Protein Crystallography Group and Membrane Protein Laboratory, Imperial College, London, UK.

Macromolecule Content

Total Structure Weight: 114.06 kDa
Atom Count: 7,869
Modelled Residue Count: 1,032
Deposited Residue Count: 1,049
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACRIFLAVIN RESISTANCE PROTEIN B	A	1,049	Escherichia coli K-12	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224 Go to UniProtKB: P31224
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31224
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DXC Query on DXC 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]	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID C₂₄ H₄₀ O₄ KXGVEGMKQFWNSR-LLQZFEROSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.85 Å
R-Value Free: 0.349 (Depositor), 0.330 (DCC)
R-Value Work: 0.278 (Depositor), 0.270 (DCC)
R-Value Observed: 0.281 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.49	α = 90
b = 145.49	β = 90
c = 515.181	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-12-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description