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- PDB-1oyd: Structural Basis of Multiple Binding Capacity of the AcrB multidr... -

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Basic information

Entry
Database: PDB / ID: 1oyd
TitleStructural Basis of Multiple Binding Capacity of the AcrB multidrug Efflux Pump
ComponentsAcriflavine resistance protein B
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic transport ...alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic 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
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
DEQUALINIUM / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsYu, E.W. / MeDermott, G. / Zgurskaya, H.I. / Nikaido, H. / Koshland Jr., D.E.
CitationJournal: Science / Year: 2003
Title: Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump.
Authors: Yu, E.W. / McDermott, G. / Zgurskaya, H.I. / Nikaido, H. / Koshland, D.E.
History
DepositionApr 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acriflavine resistance protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1222
Polymers113,6651
Non-polymers4571
Water00
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)342,3666
Polymers340,9963
Non-polymers1,3703
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 area20350 Å2
ΔGint-79 kcal/mol
Surface area115360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)144.767, 144.767, 517.891
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: 113665.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ACRB OR ACRE OR B0462 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224
#2: Chemical ChemComp-DEQ / DEQUALINIUM / DEQUADIN


Mass: 456.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H40N4

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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: 4.86 Å3/Da / Density % sol: 74.5 %
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 5.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
135 mg/mlprotein1drop
220 mMTris1droppH8.0
30.1 %DDM1drop
420 mMdithiothreitol1drop
57 %PEG40001reservoir
620-40 mMsodium citrate1reservoirpH5.6 or 6.5
720-50 mM1reservoirKNO3
810 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.78→46.61 Å / Num. all: 21326 / Num. obs: 21326 / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 3.8 Å / Num. obs: 35008 / % possible obs: 98 % / Num. measured all: 212408 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
Highest resolution: 3.8 Å / Lowest resolution: 3.94 Å / % possible obs: 99.3 % / Rmerge(I) obs: 0.538

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→46.6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.338 --
Rwork0.284 --
all0.287 --
obs0.287 20243 100 %
Refinement stepCycle: LAST / Resolution: 3.8→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7639 0 34 0 7673
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 46.6 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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