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- PDB-2hqd: Conformation of the AcrB Multidrug Efflux Pump in Mutants of the ... -

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Basic information

Entry
Database: PDB / ID: 2hqd
TitleConformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway
ComponentsAcriflavine resistance protein B
KeywordsMEMBRANE PROTEIN / multidrug efflux pump
Function / homology
Function and homology information


alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport ...alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / response to toxic substance / response to xenobiotic stimulus / response to antibiotic / 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 pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / 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 K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsSu, C.-C. / Li, M. / Gu, R. / Takatsuka, Y. / McDermott, G. / Nikaido, H. / Yu, E.W.
CitationJournal: J.Bacteriol. / Year: 2006
Title: Conformation of the AcrB multidrug efflux pump in mutants of the putative proton relay pathway
Authors: Su, C.-C. / Li, M. / Gu, R. / Takatsuka, Y. / McDermott, G. / Nikaido, H. / Yu, E.W.
History
DepositionJul 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)114,1741
Polymers114,1741
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)342,5213
Polymers342,5213
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area20690 Å2
ΔGint-93 kcal/mol
Surface area116680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)145.035, 145.035, 513.672
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 / AcrB membrane transporter


Mass: 114173.742 Da / Num. of mol.: 1 / Mutation: D408A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: acrB, acrE, b0462 / Plasmid: pSPORT1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(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: 4.57 Å3/Da / Density % sol: 73.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9799
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2005
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. obs: 585851 / % possible obs: 94.7 % / Observed criterion σ(I): 1.3
Reflection shellResolution: 3.65→3.78 Å / % possible all: 92.3

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T9U

1t9u


Resolution: 3.65→20 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.864 / SU B: 28.622 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.725 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1093 5.2 %RANDOM
Rwork0.261 ---
obs0.263 20020 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 100.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å2-0.71 Å20 Å2
2---1.41 Å20 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 3.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7718 0 0 0 7718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0910.0227862
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg6.5851.96910678
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg24.18251014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.71224.477306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg30.609151327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4581538
X-RAY DIFFRACTIONr_chiral_restr0.4840.21264
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.025821
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.5140.27233
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.4290.25038
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.460.2528
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5030.2132
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4290.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0361.55540
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.50428124
X-RAY DIFFRACTIONr_scbond_it6.93933193
X-RAY DIFFRACTIONr_scangle_it9.9724.52554
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.65→3.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 76 -
Rwork0.342 1510 -
obs--94.91 %

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