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- PDB-4dx6: Transport of drugs by the multidrug transporter AcrB involves an ... -

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Basic information

Entry
Database: PDB / ID: 4dx6
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


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 / 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
Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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)384,58912
Polymers381,0155
Non-polymers3,5747
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.690, 165.450, 245.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acriflavine resistance protein B


Mass: 114793.336 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) / Gene: artificial gene / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): Xl1blue
#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

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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: 3.88 Å3/Da / Density % sol: 68.31 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M ADA, pH 6.5 0.2M ammonium sulfate 9% PEG 4000 6% glycerol , 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: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→49.28 Å / Num. all: 252360 / Num. obs: 252313 / % possible obs: 90.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.29 / Net I/σ(I): 4.09
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.29-2.430.0430.13159.6
2.43-2.590.0430.22185.2
2.59-2.80.0430.43198.1
2.8-3.070.0430.93199.8
3.07-3.430.0432.03199.8
3.43-3.960.0434.92199.8
3.96-4.840.04310.5199.7
4.84-6.810.04311.83199.9
6.81-49.280.04327.12199.5

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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: 2.9→49.28 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.47 / σ(F): 1.02 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2703 12679 5 %
Rwork0.2086 --
obs0.2116 252313 99.8 %
all-252360 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.152 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.5755 Å20 Å2-0 Å2
2--10.9588 Å2-0 Å2
3----5.3833 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25987 0 245 0 26232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00926729
X-RAY DIFFRACTIONf_angle_d1.2636289
X-RAY DIFFRACTIONf_dihedral_angle_d17.4559629
X-RAY DIFFRACTIONf_chiral_restr0.0794297
X-RAY DIFFRACTIONf_plane_restr0.0054617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9330.38274240.33618020X-RAY DIFFRACTION100
2.933-2.96750.3914260.33738049X-RAY DIFFRACTION100
2.9675-3.00370.38354170.32627950X-RAY DIFFRACTION100
3.0037-3.04170.39054290.32838026X-RAY DIFFRACTION100
3.0417-3.08170.38414220.30598047X-RAY DIFFRACTION100
3.0817-3.12390.35214270.28598038X-RAY DIFFRACTION100
3.1239-3.16850.33614210.2728041X-RAY DIFFRACTION100
3.1685-3.21580.32924220.27088017X-RAY DIFFRACTION100
3.2158-3.2660.31984220.27528009X-RAY DIFFRACTION100
3.266-3.31960.34884260.26378097X-RAY DIFFRACTION100
3.3196-3.37680.3084160.24978005X-RAY DIFFRACTION100
3.3768-3.43820.28214250.23688072X-RAY DIFFRACTION100
3.4382-3.50430.30624210.2317963X-RAY DIFFRACTION100
3.5043-3.57580.28394240.21688031X-RAY DIFFRACTION100
3.5758-3.65350.27384210.21298040X-RAY DIFFRACTION100
3.6535-3.73850.27824260.20678050X-RAY DIFFRACTION100
3.7385-3.8320.25044200.18038010X-RAY DIFFRACTION100
3.832-3.93550.26864280.18788051X-RAY DIFFRACTION100
3.9355-4.05130.26864220.18067952X-RAY DIFFRACTION100
4.0513-4.1820.2564150.18028050X-RAY DIFFRACTION100
4.182-4.33140.23794240.17468039X-RAY DIFFRACTION100
4.3314-4.50470.23864210.16778006X-RAY DIFFRACTION100
4.5047-4.70950.21444230.15528038X-RAY DIFFRACTION100
4.7095-4.95760.20894260.14567966X-RAY DIFFRACTION100
4.9576-5.26790.23964250.16988041X-RAY DIFFRACTION100
5.2679-5.67410.27094220.20028048X-RAY DIFFRACTION100
5.6741-6.24410.27764150.19628045X-RAY DIFFRACTION100
6.2441-7.14530.23224230.17258029X-RAY DIFFRACTION100
7.1453-8.99330.19454190.13038018X-RAY DIFFRACTION100
8.9933-49.28730.23154270.22397997X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 40.4434 Å / Origin y: -30.4317 Å / Origin z: -31.0562 Å
111213212223313233
T-0.2169 Å20.0078 Å2-0.1132 Å2-0.2054 Å20.0536 Å2---0.0819 Å2
L0.4395 °20.007 °20.0397 °2-0.1586 °2-0.128 °2--0.3131 °2
S0.1958 Å °0.2818 Å °0.1491 Å °-0.1933 Å °-0.1168 Å °-0.0122 Å °-0.103 Å °-0.0035 Å °-0.0209 Å °
Refinement TLS groupSelection details: all

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