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- PDB-1t9y: Structural Basis of Multidrug Transport by the AcrB Multidrug Eff... -

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Basic information

Entry
Database: PDB / ID: 1t9y
TitleStructural Basis of Multidrug Transport by the AcrB Multidrug Efflux Pump
ComponentsAcriflavine resistance protein B
KeywordsMEMBRANE PROTEIN / 12 transmembranes
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
Chem-MC2 / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.64 Å
AuthorsYu, E.W. / McDermott, G. / Nikaido, H.
CitationJournal: J.Bacteriol. / Year: 2005
Title: A Periplasmic Drug-Binding Site of the AcrB Multidrug Efflux Pump: a Crystallographic and Site-Directed Mutagenesis Study
Authors: Yu, E.W. / Aires, J.R. / McDermott, G. / Nikaido, H.
History
DepositionMay 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 31, 2018Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / pdbx_struct_assembly ...database_PDB_caveat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_prop.biol_id
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acriflavine resistance protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5153
Polymers113,6221
Non-polymers8932
Water0
1
A: Acriflavine resistance protein B
hetero molecules

A: Acriflavine resistance protein B
hetero molecules

A: Acriflavine resistance protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,5469
Polymers340,8663
Non-polymers2,6796
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area22560 Å2
ΔGint-80 kcal/mol
Surface area116020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.922, 144.922, 516.675
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 Acriflavine resistance protein B


Mass: 113622.148 Da / Num. of mol.: 1 / Mutation: N109A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acrB,acrE,b0462 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224
#2: Chemical ChemComp-MC2 / N2-(L-PHENYLALANYL)-N1-(NAPHTHALENYL)-L-ARIGNINAMIDE


Mass: 446.545 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H30N6O2

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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: 4.59 Å3/Da / Density % sol: 73.22 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.64→182.57 Å / Num. all: 464493 / Num. obs: 34163 / % possible obs: 100 % / Observed criterion σ(F): 5.5 / Observed criterion σ(I): 5.5
Reflection shellResolution: 3.64→3.83 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.64→182.57 Å / Rfactor Rfree: 0.33959 / Rfactor Rwork: 0.27663 / Rfactor all: 0.2794 / Rfactor obs: 0.27762
Refinement stepCycle: LAST / Resolution: 3.64→182.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7718 0 66 0 7784

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