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- PDB-8px7: Structure of Bacterial Multidrug Efflux transporter AcrB, solved ... -

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Basic information

Entry
Database: PDB / ID: 8px7
TitleStructure of Bacterial Multidrug Efflux transporter AcrB, solved at wavelength 3.02 A
ComponentsMultidrug efflux pump subunit AcrB
KeywordsMEMBRANE PROTEIN / efflux pump
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
Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsEl Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C. / Qu, F. / Beis, K. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multidrug efflux pump subunit AcrB


Theoretical massNumber of molelcules
Total (without water)114,2181
Polymers114,2181
Non-polymers00
Water0
1
A: Multidrug efflux pump subunit AcrB

A: Multidrug efflux pump subunit AcrB

A: Multidrug efflux pump subunit AcrB


Theoretical massNumber of molelcules
Total (without water)342,6533
Polymers342,6533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area20480 Å2
ΔGint-103 kcal/mol
Surface area116260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.300, 145.300, 516.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 114217.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / 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: 4.6 Å3/Da / Density % sol: 73.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 4000, 0.1 M HEPES PH 7.5, 0.1 M AMMONIUM SULPHATE AND 22% V/V GLYCEROL

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.024 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 3.024 Å / Relative weight: 1
ReflectionResolution: 3.4→28.94 Å / Num. obs: 29410 / % possible obs: 99.7 % / Redundancy: 86.9 % / Biso Wilson estimate: 132.83 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1595 / Rpim(I) all: 0.01721 / Rrim(I) all: 0.1604 / Net I/σ(I): 31.15
Reflection shellResolution: 3.4→3.521 Å / Redundancy: 73.1 % / Rmerge(I) obs: 0.1595 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 2892 / CC1/2: 0.52 / Rpim(I) all: 0.01721 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 3.4→28.94 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.88 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.528
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1502 5.11 %RANDOM
Rwork0.301 ---
obs0.302 29404 100 %-
Displacement parametersBiso mean: 180.06 Å2
Baniso -1Baniso -2Baniso -3
1--9.6499 Å20 Å20 Å2
2---9.6499 Å20 Å2
3---19.2997 Å2
Refine analyzeLuzzati coordinate error obs: 0.76 Å
Refinement stepCycle: 1 / Resolution: 3.4→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7854 0 0 0 7854
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098004HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0110870HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2730SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1346HARMONIC5
X-RAY DIFFRACTIONt_it8004HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.81
X-RAY DIFFRACTIONt_other_torsion16.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1082SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9207SEMIHARMONIC4
LS refinement shellResolution: 3.4→3.42 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3245 -3.74 %
Rwork0.288 567 -
all0.2893 589 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 11.8532 Å / Origin y: 61.1108 Å / Origin z: 228.483 Å
111213212223313233
T0.3526 Å20.0665 Å2-0.077 Å2-0.3159 Å2-0.1169 Å2--0.2759 Å2
L0.4716 °2-0.135 °20.1842 °2-0.4933 °20.2906 °2--0.9168 °2
S0.0606 Å °0.1555 Å °-0.3103 Å °-0.0777 Å °-0.0315 Å °0.1147 Å °0.0981 Å °0.1727 Å °-0.029 Å °
Refinement TLS groupSelection details: { A|* }

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