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- PDB-2i6w: Crystal structure of the multidrug efflux transporter AcrB -

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Basic information

Entry
Database: PDB / ID: 2i6w
TitleCrystal structure of the multidrug efflux transporter AcrB
ComponentsAcriflavine resistance protein B
KeywordsTRANSPORT PROTEIN / Membrane protein / multidrug efflux transporter / AcrB
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / outer membrane-bounded periplasmic space / identical protein binding / membrane / plasma membrane
Similarity search - Function
Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.1 Å
AuthorsDas, D. / Xu, Q.S. / Kim, S.H.
CitationJournal: J.Struct.Biol. / Year: 2007
Title: Crystal structure of the multidrug efflux transporter AcrB at 3.1A resolution reveals the N-terminal region with conserved amino acids.
Authors: Das, D. / Xu, Q.S. / Lee, J.Y. / Ankoudinova, I. / Huang, C. / Lou, Y. / Degiovanni, A. / Kim, R. / Kim, S.H.
History
DepositionAug 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acriflavine resistance protein B


Theoretical massNumber of molelcules
Total (without water)113,6651
Polymers113,6651
Non-polymers00
Water00
1
A: Acriflavine resistance protein B

A: Acriflavine resistance protein B

A: Acriflavine resistance protein B


Theoretical massNumber of molelcules
Total (without water)340,9963
Polymers340,9963
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area19560 Å2
ΔGint-90 kcal/mol
Surface area111030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)146.300, 146.300, 514.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Acriflavine resistance protein B


Mass: 113665.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Membrane protein / Source: (natural) Escherichia coli (E. coli) / Strain: BL21(DE3) / References: UniProt: P31224

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.68 Å3/Da / Density % sol: 73.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.1 M Sodium chloride, 0.1 M Lithium sulfate, 12% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99186 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 15, 2006 / Details: MIRRORS
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99186 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 48061 / Num. obs: 48061 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 66.7 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.117 / Net I/σ(I): 16.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 3.1→45.12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 5460865.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.341 1952 5 %RANDOM
Rwork0.305 ---
obs0.305 38899 99.6 %-
all-41661 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.6032 Å2 / ksol: 0.252892 e/Å3
Displacement parametersBiso mean: 69.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.77 Å216.87 Å20 Å2
2--10.77 Å20 Å2
3----21.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.68 Å0.57 Å
Luzzati d res low-50 Å
Luzzati sigma a0.55 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3.1→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7737 0 0 0 7737
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.476 289 4.5 %
Rwork0.42 6113 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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