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- PDB-4dx7: Transport of drugs by the multidrug transporter AcrB involves an ... -

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Basic information

Entry
Database: PDB / ID: 4dx7
TitleTransport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop
Components
  • Acriflavine resistance protein B
  • DARPIN
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / DARPin / multidrug efflux 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 / 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 / Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DECANE / DODECANE / DOXORUBICIN / HEXANE / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.253 Å
AuthorsEicher, T. / Cha, H. / Seeger, M.A. / Brandstaetter, L. / El-Delik, J. / Bohnert, J.A. / Kern, W.V. / Verrey, F. / Gruetter, M.G. / Diederichs, K. / Pos, K.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop.
Authors: Eicher, T. / Cha, H.J. / Seeger, M.A. / Brandstatter, L. / El-Delik, J. / Bohnert, J.A. / Kern, W.V. / Verrey, F. / Grutter, M.G. / Diederichs, K. / Pos, K.M.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Source and taxonomy
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
D: DARPIN
E: DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,25929
Polymers380,8445
Non-polymers7,41524
Water30,6261700
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.943, 163.285, 245.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 5 molecules ABCDE

#1: Protein Acriflavine resistance protein B


Mass: 114736.289 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, JW0451 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P31224
#2: Protein DARPIN /


Mass: 18317.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): Xl1blue

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Sugars , 2 types, 8 molecules

#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#7: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 6 types, 1716 molecules

#4: Chemical ChemComp-DM2 / DOXORUBICIN / ADRIAMYCIN / Doxorubicin


Mass: 543.519 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H29NO11 / Comment: medication, chemotherapy*YM
#5: Chemical
ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26
#6: Chemical
ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1700 / 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: 3.84 Å3/Da / Density % sol: 68.01 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.025M ADA, pH 6.5, 0.2M ammonium sulfate, 7.66% PEG 4000, 8.8% glycerol, 0.004M doxorubicin, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→49.153 Å / Num. all: 274592 / Num. obs: 274585 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.94
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.25-2.390.9841.75197.3
2.39-2.550.7123.131100
2.55-2.760.4414.971100
2.76-3.020.2448.541100
3.02-3.370.13514.481100
3.37-3.890.07125.271100
3.89-4.760.04537.641100
4.76-6.70.04239.721100
6.7-49.1530.0348.42198.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.253→49.093 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.99 / Phase error: 22.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 13724 5 %
Rwork0.1849 --
obs0.187 274555 99.52 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.01 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.6515 Å20 Å2-0 Å2
2--8.8845 Å2-0 Å2
3----3.233 Å2
Refinement stepCycle: LAST / Resolution: 2.253→49.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25979 0 515 1700 28194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726990
X-RAY DIFFRACTIONf_angle_d1.0536616
X-RAY DIFFRACTIONf_dihedral_angle_d14.6629728
X-RAY DIFFRACTIONf_chiral_restr0.0684322
X-RAY DIFFRACTIONf_plane_restr0.0044620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2527-2.27830.34083920.31167546X-RAY DIFFRACTION87
2.2783-2.30510.3384580.27858698X-RAY DIFFRACTION100
2.3051-2.33320.32164520.26928623X-RAY DIFFRACTION100
2.3332-2.36270.30474590.26248656X-RAY DIFFRACTION100
2.3627-2.39380.30994610.24858633X-RAY DIFFRACTION100
2.3938-2.42660.28554520.24378665X-RAY DIFFRACTION100
2.4266-2.46130.31744580.24168690X-RAY DIFFRACTION100
2.4613-2.4980.28454520.22918642X-RAY DIFFRACTION100
2.498-2.5370.27254730.2178688X-RAY DIFFRACTION100
2.537-2.57860.27024410.21978686X-RAY DIFFRACTION100
2.5786-2.62310.28264560.21038662X-RAY DIFFRACTION100
2.6231-2.67080.24514650.19348725X-RAY DIFFRACTION100
2.6708-2.72210.24274500.19058681X-RAY DIFFRACTION100
2.7221-2.77770.25554570.19328657X-RAY DIFFRACTION100
2.7777-2.83810.24974620.18638742X-RAY DIFFRACTION100
2.8381-2.90410.23144550.17868660X-RAY DIFFRACTION100
2.9041-2.97670.21984560.17488731X-RAY DIFFRACTION100
2.9767-3.05720.24164610.17728694X-RAY DIFFRACTION100
3.0572-3.14710.21754610.16768714X-RAY DIFFRACTION100
3.1471-3.24870.21524600.16438743X-RAY DIFFRACTION100
3.2487-3.36480.21574510.17218727X-RAY DIFFRACTION100
3.3648-3.49950.22354720.17218744X-RAY DIFFRACTION100
3.4995-3.65870.20944550.16748746X-RAY DIFFRACTION100
3.6587-3.85150.20314560.16438770X-RAY DIFFRACTION100
3.8515-4.09270.20684660.16988762X-RAY DIFFRACTION100
4.0927-4.40850.19264650.16218818X-RAY DIFFRACTION100
4.4085-4.85180.19024600.15298833X-RAY DIFFRACTION100
4.8518-5.55310.19994690.16518842X-RAY DIFFRACTION100
5.5531-6.99310.23954710.20028950X-RAY DIFFRACTION100
6.9931-49.10430.20914780.19179103X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 40.481 Å / Origin y: -31.4143 Å / Origin z: -30.5952 Å
111213212223313233
T0.1179 Å20.0074 Å2-0.0115 Å2-0.1765 Å2-0.0331 Å2--0.1554 Å2
L0.3865 °20.0445 °2-0.0621 °2-0.2373 °2-0.1084 °2--0.3479 °2
S0.0582 Å °0.0139 Å °0.0648 Å °-0.003 Å °-0.0405 Å °0.0353 Å °-0.0484 Å °0.0295 Å °-0.0125 Å °
Refinement TLS groupSelection details: all

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