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- PDB-3aoa: Structures of the multidrug exporter AcrB reveal a proximal multi... -

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Basic information

Entry
Database: PDB / ID: 3aoa
TitleStructures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket
ComponentsAcriflavine resistance protein B
KeywordsMEMBRANE PROTEIN / Inner Membrane
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 / membrane / identical protein binding / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.35 Å
AuthorsNakashima, R. / Sakurai, K. / Yamaguchi, A.
CitationJournal: Nature / Year: 2011
Title: Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket
Authors: Nakashima, R. / Sakurai, K. / Yamasaki, S. / Nishino, K. / Yamaguchi, A.
History
DepositionSep 23, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acriflavine resistance protein B
B: Acriflavine resistance protein B
C: Acriflavine resistance protein B


Theoretical massNumber of molelcules
Total (without water)342,6533
Polymers342,6533
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18620 Å2
ΔGint-75 kcal/mol
Surface area116900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.533, 134.438, 162.783
Angle α, β, γ (deg.)90.00, 97.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Acriflavine resistance protein B


Mass: 114217.742 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: acrB, acrE, b0462, EcDH1_3148, JW0451 / Plasmid: pBAD33 / Production host: Escherichia coli (E. coli) / Strain (production host): MG1655 / References: UniProt: P31224
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 3.58 Å3/Da / Density % sol: 65.68 % / Mosaicity: 0.438 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 20mM sodium phosphate, 100mM NaCl, 14 %(w/v) PEG 4000, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 15, 2010
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 68812 / % possible obs: 99.4 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.063 / Χ2: 1.717 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.35-3.417.60.37334511.5141100
3.41-3.477.60.33234561.5181100
3.47-3.547.60.29434411.5031100
3.54-3.617.70.23534401.571100
3.61-3.697.60.19534391.571100
3.69-3.777.60.17234441.5491100
3.77-3.877.60.13834711.5061100
3.87-3.977.60.11834191.5321100
3.97-4.097.60.09934381.5351100
4.09-4.227.60.08534511.587199.9
4.22-4.377.60.07534591.702199.9
4.37-4.557.60.06234511.767199.8
4.55-4.757.60.05834241.736199.9
4.75-57.60.05134581.697199.8
5-5.327.70.05134671.646199.9
5.32-5.737.70.05734571.8091100
5.73-6.37.60.06134772.3011100
6.3-7.217.30.05334762.5731100
7.21-9.087.40.03834922.252199.7
9.08-506.90.02632011.461189.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.65 Å49.28 Å
Translation3.65 Å49.28 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DHH

2dhh


Resolution: 3.35→49.3 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.3124 / WRfactor Rwork: 0.2667 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7115 / SU B: 34.895 / SU ML: 0.566 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.674 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.32582 3411 5 %RANDOM
Rwork0.27137 ---
obs0.27419 64414 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 192.66 Å2 / Biso mean: 118.858 Å2 / Biso min: 32.97 Å2
Baniso -1Baniso -2Baniso -3
1-13.43 Å20 Å28.63 Å2
2---8.89 Å20 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 3.35→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23322 0 0 3 23325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02223760
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.581.96832268
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87553060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.06224.484930
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.292154008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.67415114
X-RAY DIFFRACTIONr_chiral_restr0.0970.23813
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117601
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.551.515201
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.025224525
X-RAY DIFFRACTIONr_scbond_it1.0538559
X-RAY DIFFRACTIONr_scangle_it1.9044.57743
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.345→3.432 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 206 -
Rwork0.397 4091 -
all-4297 -
obs--84.49 %

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