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- PDB-9fhc: Crystallographic structure of AcrB V612F with bound minocycline -

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Basic information

Entry
Database: PDB / ID: 9fhc
TitleCrystallographic structure of AcrB V612F with bound minocycline
Components
  • DARPIN
  • Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / Drug efflux / RND transporter
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
Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
Chem-MIY / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLazarova, M. / Diederichs, K. / Pos, K.M.
Funding support Switzerland, Germany, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation3100A0_118402 Switzerland
German Research Foundation (DFG)SFB807-P18 Germany
German Research Foundation (DFG)SFB1507-P3 Germany
German Research Foundation (DFG)DFG-EXC115 Germany
CitationJournal: To Be Published
Title: Crystallographic structure of AcrB V612F with bound minocycline
Authors: Lazarova, M. / Diederichs, K. / Pos, K.M.
History
DepositionMay 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: 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
B: DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5593
Polymers133,1022
Non-polymers4571
Water5,062281
1
A: Multidrug efflux pump subunit AcrB
B: DARPIN
hetero molecules

A: Multidrug efflux pump subunit AcrB
B: DARPIN
hetero molecules

A: Multidrug efflux pump subunit AcrB
B: DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,6789
Polymers399,3066
Non-polymers1,3723
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)227.460, 227.460, 227.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 114784.336 Da / Num. of mol.: 1 / Mutation: V612F
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
#2: Protein DARPIN


Mass: 18317.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-MIY / (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE / MINOCYCLINE


Mass: 457.476 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N3O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.68 Å3/Da / Density % sol: 66.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M sodium acetate pH 4.5, 3-7% PEG200, 15-25% PEG400, 0.15M MgCl2, 0.15M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→29.87 Å / Num. obs: 93149 / % possible obs: 94.51 % / Redundancy: 24.9 % / CC1/2: 0.999 / Net I/σ(I): 27.16
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 6554 / CC1/2: 0.822

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.87 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.238 4657 -
Rwork0.208 --
obs-93134 94.51 %
Refinement stepCycle: LAST / Resolution: 2.2→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9115 0 33 281 9429
LS refinement shellResolution: 2.2→2.279 Å
RfactorNum. reflection% reflection
Rfree0.3336 --
Rwork0.2674 --
obs-6554 67.04 %

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