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- PDB-5yil: Hoisting-loop in bacterial multidrug exporter AcrB is a highly fl... -

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Basic information

Entry
Database: PDB / ID: 5yil
TitleHoisting-loop in bacterial multidrug exporter AcrB is a highly flexible hinge that enables the large motion of the subdomains
ComponentsMultidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / Transporter / RND-type transporter / Multidrug efflux / bacteria / Escherichia coli / Membrane 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 / xenobiotic transmembrane transporter activity / efflux 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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZwama, M. / Sakurai, K. / Hayashi, K. / Nakashima, R. / Kitagawa, K. / Nishino, K. / Yamaguchi, A.
CitationJournal: Front Microbiol / Year: 2017
Title: Hoisting-Loop in Bacterial Multidrug Exporter AcrB Is a Highly Flexible Hinge That Enables the Large Motion of the Subdomains.
Authors: Zwama, M. / Hayashi, K. / Sakurai, K. / Nakashima, R. / Kitagawa, K. / Nishino, K. / Yamaguchi, A.
History
DepositionOct 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multidrug efflux pump subunit AcrB
B: Multidrug efflux pump subunit AcrB
C: Multidrug efflux pump subunit AcrB


Theoretical massNumber of molelcules
Total (without water)341,5873
Polymers341,5873
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-80 kcal/mol
Surface area114830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.980, 139.810, 285.450
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 Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 113862.367 Da / Num. of mol.: 3 / Mutation: 868, 871-872 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / 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: 3.96 Å3/Da / Density % sol: 68.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 20MM SODIUM PHOSPHATE, 100MM NACL, 14%(W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 14, 2016
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 98346 / % possible obs: 94.8 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 18.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.013 / % possible all: 83.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AOA

3aoa


Resolution: 3→100 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.882 / SU B: 17.494 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R: 1.674 / ESU R Free: 0.416 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27318 5112 4.9 %RANDOM
Rwork0.22371 ---
obs0.22618 98346 94.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 86.539 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23569 0 0 0 23569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01924021
X-RAY DIFFRACTIONr_bond_other_d0.0020.0223015
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.96732618
X-RAY DIFFRACTIONr_angle_other_deg1.138353231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.80253098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.09524.5940
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.438154045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.08215112
X-RAY DIFFRACTIONr_chiral_restr0.0940.23837
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02126711
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024753
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.268.59512401
X-RAY DIFFRACTIONr_mcbond_other6.2548.59412400
X-RAY DIFFRACTIONr_mcangle_it9.9812.87715496
X-RAY DIFFRACTIONr_mcangle_other9.98212.87815497
X-RAY DIFFRACTIONr_scbond_it5.4488.96211620
X-RAY DIFFRACTIONr_scbond_other5.4458.96211620
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.85913.29217122
X-RAY DIFFRACTIONr_long_range_B_refined16.08997375
X-RAY DIFFRACTIONr_long_range_B_other16.08897374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 358 -
Rwork0.301 6635 -
obs--87.6 %

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