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- PDB-3w9h: Structural basis for the inhibition of bacterial multidrug exporters -

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Basic information

Entry
Database: PDB / ID: 3w9h
TitleStructural basis for the inhibition of bacterial multidrug exporters
ComponentsAcriflavine resistance protein B
KeywordsMEMBRANE PROTEIN / AcrB / Efflux pump / Transporter / Multidrug efflux pump / AcrA / TolC / Inner Membrane / Transport protein
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 / 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
Chem-P9D / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 Å
AuthorsSakurai, K. / Nagata, C. / Nakashima, R. / Yamaguchi, A.
CitationJournal: Nature / Year: 2013
Title: Structural basis for the inhibition of bacterial multidrug exporters
Authors: Nakashima, R. / Sakurai, K. / Yamasaki, S. / Hayashi, K. / Nagata, C. / Hoshino, K. / Onodera, Y. / Nishino, K. / Yamaguchi, A.
History
DepositionApr 4, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)335,9024
Polymers335,2093
Non-polymers6941
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18460 Å2
ΔGint-78 kcal/mol
Surface area115180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.279, 134.160, 162.202
Angle α, β, γ (deg.)90.000, 97.830, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Acriflavine resistance protein B


Mass: 111736.180 Da / Num. of mol.: 3 / Fragment: UNP residues 1-1033
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: acrB, acrE, b0462, JW0451 / Plasmid: pUC118 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224
#2: Chemical ChemComp-P9D / [{2-[({[(3R)-1-{8-[(4-tert-butyl-1,3-thiazol-2-yl)carbamoyl]-4-oxo-3-[(E)-2-(1H-tetrazol-5-yl)ethenyl]-4H-pyrido[1,2-a]pyrimidin-2-yl}piperidin-3-yl]oxy}carbonyl)amino]ethyl}(dimethyl)ammonio]acetate


Mass: 693.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H39N11O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.64 Å3/Da / Density % sol: 66.19 % / Mosaicity: 0.698 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 20mM sodium phosphate, 100mM NaCl, 14% PEG 4000, 32ug/ml ABI-PP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 89374 / % possible obs: 97.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Χ2: 1.336 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.05-3.13.40.62244260.93197.8
3.1-3.163.40.50644390.94198.1
3.16-3.223.40.39644770.962197.9
3.22-3.293.40.33245080.998198
3.29-3.363.40.27744551.062198.3
3.36-3.433.40.22244451.129197.9
3.43-3.523.40.19244831.218198.1
3.52-3.623.40.15344631.211198.2
3.62-3.723.40.12844801.401198.2
3.72-3.843.40.10444981.335198.5
3.84-3.983.40.0944921.499198.3
3.98-4.143.40.07244741.522198.5
4.14-4.333.40.05944931.622198.2
4.33-4.563.50.04945241.746198.6
4.56-4.843.60.04344931.674198.6
4.84-5.213.60.03945411.562198.9
5.21-5.743.70.03845831.41199.7
5.74-6.573.70.03545981.404199.7
6.57-8.273.70.02745841.43199.4
8.27-503.30.02339181.548183.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.39 Å42.67 Å
Translation3.39 Å42.67 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V50

2v50


Resolution: 3.05→43.01 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.2832 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6837 / SU B: 25.799 / SU ML: 0.444 / SU Rfree: 0.5282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.528 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3168 4430 5 %RANDOM
Rwork0.2313 ---
obs0.2356 88240 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 233.73 Å2 / Biso mean: 105.2331 Å2 / Biso min: 29.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20.03 Å2
2---0.02 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.05→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23550 0 49 15 23614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01924053
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.97132672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00853096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93124.537939
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.621154041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.23215111
X-RAY DIFFRACTIONr_chiral_restr0.1070.23840
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117864
LS refinement shellResolution: 3.047→3.126 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 312 -
Rwork0.348 5908 -
all-6220 -
obs--92.49 %

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