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

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Basic information

Entry
Database: PDB / ID: 3aod
TitleStructures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket
ComponentsAcriflavine resistance protein B
KeywordsMEMBRANE PROTEIN/ANTIBIOTIC / Membrane Protein / Inner Membrane / MEMBRANE PROTEIN-ANTIBIOTIC complex
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic transmembrane transporter activity / efflux 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
Chem-MIY / RIFAMPICIN / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 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 ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)343,9345
Polymers342,6533
Non-polymers1,2802
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18630 Å2
ΔGint-76 kcal/mol
Surface area116860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.604, 134.496, 162.833
Angle α, β, γ (deg.)90.00, 97.75, 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) / Gene: acrB, acrE, b0462, EcDH1_3148, JW0451 / Plasmid: pBAD33 / Production host: Escherichia coli (E. coli) / Strain (production host): MG1655 / References: UniProt: P31224
#2: Chemical ChemComp-MIY / (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE / MINOCYCLINE / Minocycline


Mass: 457.476 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N3O7 / Comment: medication, antibiotic*YM
#3: Chemical ChemComp-RFP / RIFAMPICIN / Rifampicin


Mass: 822.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H58N4O12 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.59 Å3/Da / Density % sol: 65.72 % / Mosaicity: 0.242 °
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: Jun 4, 2010
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 71816 / % possible obs: 99.3 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.064 / Χ2: 2 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.3-3.367.60.34535931.7481100
3.36-3.427.60.28435681.7621100
3.42-3.487.60.25636132.2351100
3.48-3.557.60.21736261.7551100
3.55-3.637.60.17735791.7881100
3.63-3.727.60.15335741.7331100
3.72-3.817.60.12736121.771100
3.81-3.917.50.11235911.7021100
3.91-4.037.50.09135991.6941100
4.03-4.167.50.07935991.7651100
4.16-4.317.50.0736122.0111100
4.31-4.487.40.06736352.1781100
4.48-4.687.30.0736082.6551100
4.68-4.937.10.06136082.6821100
4.93-5.2470.0636212.7091100
5.24-5.647.10.06436062.7851100
5.64-6.217.40.06136352.6161100
6.21-7.17.50.03836431.6171100
7.1-8.947.40.02636401.383199.7
8.94-506.30.02432541.469187.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å47.25 Å
Translation3.5 Å47.25 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: 3.3→47.5 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.869 / WRfactor Rfree: 0.3048 / WRfactor Rwork: 0.2515 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7395 / SU B: 29.404 / SU ML: 0.488 / SU Rfree: 0.6355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.635 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.31768 3532 5 %RANDOM
Rwork0.25784 ---
obs0.26089 67196 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 182.53 Å2 / Biso mean: 103.983 Å2 / Biso min: 28.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.06 Å2
2--0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 3.3→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23322 0 92 5 23419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02223859
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.97332420
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73553060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.81224.484930
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.085154008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.81915114
X-RAY DIFFRACTIONr_chiral_restr0.1030.23832
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117678
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_it0.6111.515201
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.143224525
X-RAY DIFFRACTIONr_scbond_it1.22338658
X-RAY DIFFRACTIONr_scangle_it2.2054.57895
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.303→3.389 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 224 -
Rwork0.372 4600 -
all-4824 -
obs--95.49 %

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