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- PDB-9fe2: Crystallographic structure of AcrB V612W with bound minocycline -

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Basic information

Entry
Database: PDB / ID: 9fe2
TitleCrystallographic structure of AcrB V612W 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 speciessynthetic construct (others)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsLazarova, M. / 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 V612W with bound minocycline
Authors: Lazarova, M. / Pos, K.M.
History
DepositionMay 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: DARPIN
A: Multidrug efflux pump subunit AcrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5983
Polymers133,1412
Non-polymers4571
Water6,918384
1
D: DARPIN
A: Multidrug efflux pump subunit AcrB
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)400,7959
Polymers399,4236
Non-polymers1,3723
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Unit cell
Length a, b, c (Å)227.497, 227.497, 227.497
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 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)
#2: Protein Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 114823.367 Da / Num. of mol.: 1 / Mutation: V612W
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
#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: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 66.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH 6.5, 5.5-20.5% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.99182 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99182 Å / Relative weight: 1
ReflectionResolution: 1.89→46.44 Å / Num. obs: 155079 / % possible obs: 96.99 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 21.91
Reflection shellResolution: 1.89→1.958 Å / Num. unique obs: 15464 / CC1/2: 0.297 / CC star: 0.677

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→46.44 Å / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2436 1998 -
Rwork0.2224 --
obs-150440 96.38 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9082 0 33 384 9499
LS refinement shellResolution: 1.89→1.93 Å

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