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- PDB-2dr6: Crystal structure of a multidrug transporter reveal a functionall... -

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Basic information

Entry
Database: PDB / ID: 2dr6
TitleCrystal structure of a multidrug transporter reveal a functionally rotating mechanism
ComponentsACRB
KeywordsMEMBRANE PROTEIN / membrane transporter / multidrug efflux / drug resistance / transporter / exporter / antiporter
Function / homology
Function and homology information


alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic transport ...alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic 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 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
DOXORUBICIN / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 3.3 Å
AuthorsMurakami, S. / Nakashima, R. / Yamashita, E. / Matsumoto, T.
CitationJournal: Nature / Year: 2006
Title: Crystal structures of a multidrug transporter reveal a functionally rotating mechanism
Authors: Murakami, S. / Nakashima, R. / Yamashita, E. / Matsumoto, T. / Yamaguchi, A.
History
DepositionJun 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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
Remark 650HELIX determination method: Author determined.
Remark 700SHEET determination method: Author determined.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACRB
B: ACRB
C: ACRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,1974
Polymers342,6533
Non-polymers5441
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19190 Å2
ΔGint-85 kcal/mol
Surface area115990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.046, 134.561, 161.697
Angle α, β, γ (deg.)90.00, 98.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ACRB / multidrug efflux transporter / 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) / Plasmid: PUC-118 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P31224
#2: Chemical ChemComp-DM2 / DOXORUBICIN / ADRIAMYCIN


Mass: 543.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO11 / Comment: medication, chemotherapy*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.52 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.1 / Details: PEG4000, PH 6.1, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Apr 4, 2003
RadiationProtocol: 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: 69300 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.2
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 1.8 / % possible all: 84.2

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Processing

Software
NameVersionClassification
FFTBIGmodel building
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
FFTBIGphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 3.3→10 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.832 / SU B: 35.125 / SU ML: 0.589 / Cross valid method: THROUGHOUT / ESU R Free: 0.755 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.359 3330 5.1 %RANDOM
Rwork0.298 ---
obs0.302 62501 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 116.594 Å2
Baniso -1Baniso -2Baniso -3
1-11.21 Å20 Å22.32 Å2
2---10.34 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 3.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23322 0 39 0 23361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0420.02223806
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.6881.9732341
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.41653060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.67224.484930
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.555154008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.92115114
X-RAY DIFFRACTIONr_chiral_restr0.220.23819
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217639
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.4110.217209
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3730.215871
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3370.21560
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4640.216
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6141.516061
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.725224531
X-RAY DIFFRACTIONr_scbond_it3.70639469
X-RAY DIFFRACTIONr_scangle_it5.5694.57810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.508 230 -
Rwork0.54 4140 -
obs--91.44 %

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