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- PDB-4u95: Coupling of remote alternating-access transport mechanisms for pr... -

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Basic information

Entry
Database: PDB / ID: 4u95
TitleCoupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB
Components
  • DARPin
  • Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / DARPin / multidrug efflux protein
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
Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MIY / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPos, K.M.
CitationJournal: eLife / Year: 2014
Title: Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB
Authors: Eicher, T. / Seeger, M.A. / Anselmi, C. / Zhou, W. / Brandstaetter, L. / Verrey, F. / Diederichs, K. / Faraldo-Gomez, J.D. / Pos, K.M.
History
DepositionAug 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug efflux pump subunit AcrB
B: Multidrug efflux pump subunit AcrB
C: Multidrug efflux pump subunit AcrB
D: DARPin
E: DARPin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,6599
Polymers380,6705
Non-polymers1,9894
Water42,4612357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25680 Å2
ΔGint-92 kcal/mol
Surface area123660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.910, 162.320, 245.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 114678.195 Da / Num. of mol.: 3 / Mutation: K940A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: acrB, acrE, b0462, JW0451 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C43 / References: UniProt: P31224
#2: Protein DARPin


Mass: 18317.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: 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 / Comment: medication, antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2357 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.05M ADA, pH 6.5, 0.2 M (NH4)2SO4, 8% PEG4000, 6% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→48.993 Å / Num. obs: 349404 / % possible obs: 89.38 % / Redundancy: 7.1 % / Net I/σ(I): 11.04
Reflection shellResolution: 2→2.071 Å / Redundancy: 5.1 % / Rmerge(I) obs: 3.32 / Mean I/σ(I) obs: 0.5 / % possible all: 53.12

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERPHENIX version 1.9 -1692phasing
XDSVersion January 10, 2014data reduction
XSCALEVersion January 10, 2014data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DX5

4dx5


Resolution: 2→48.993 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 17468 5 %
Rwork0.1942 --
obs0.1963 349325 89.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→48.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25929 0 138 2357 28424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826565
X-RAY DIFFRACTIONf_angle_d1.03636092
X-RAY DIFFRACTIONf_dihedral_angle_d14.5279623
X-RAY DIFFRACTIONf_chiral_restr0.0414257
X-RAY DIFFRACTIONf_plane_restr0.0054619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9995-2.02220.38463230.38076143X-RAY DIFFRACTION50
2.0222-2.0460.39283410.36226464X-RAY DIFFRACTION53
2.046-2.0710.36323640.35266928X-RAY DIFFRACTION56
2.071-2.09720.3893890.33947377X-RAY DIFFRACTION60
2.0972-2.12480.35534100.32677812X-RAY DIFFRACTION64
2.1248-2.15390.35434400.31288353X-RAY DIFFRACTION68
2.1539-2.18470.35064730.31018973X-RAY DIFFRACTION73
2.1847-2.21730.3215080.30569660X-RAY DIFFRACTION78
2.2173-2.25190.30855490.291110452X-RAY DIFFRACTION85
2.2519-2.28890.32826040.27711492X-RAY DIFFRACTION93
2.2889-2.32830.31186430.262412203X-RAY DIFFRACTION99
2.3283-2.37070.31566490.252812322X-RAY DIFFRACTION100
2.3707-2.41630.27676480.232712308X-RAY DIFFRACTION100
2.4163-2.46560.29076500.223512320X-RAY DIFFRACTION100
2.4656-2.51920.26666440.222612273X-RAY DIFFRACTION100
2.5192-2.57780.27146520.215612359X-RAY DIFFRACTION100
2.5778-2.64220.25366480.212212314X-RAY DIFFRACTION100
2.6422-2.71370.2646500.198112367X-RAY DIFFRACTION100
2.7137-2.79350.24536510.192212362X-RAY DIFFRACTION100
2.7935-2.88370.23356520.18612381X-RAY DIFFRACTION100
2.8837-2.98670.24116500.181412361X-RAY DIFFRACTION100
2.9867-3.10630.236520.183412394X-RAY DIFFRACTION100
3.1063-3.24760.23396540.167812398X-RAY DIFFRACTION100
3.2476-3.41880.20796520.169812379X-RAY DIFFRACTION100
3.4188-3.6330.21026550.156712460X-RAY DIFFRACTION100
3.633-3.91340.18456560.151512456X-RAY DIFFRACTION100
3.9134-4.3070.19486570.151412471X-RAY DIFFRACTION100
4.307-4.92970.18286610.142412556X-RAY DIFFRACTION100
4.9297-6.20890.20136640.160812625X-RAY DIFFRACTION100
6.2089-49.00740.20246790.178612894X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 40.3928 Å / Origin y: -31.7927 Å / Origin z: -30.695 Å
111213212223313233
T0.046 Å20.0072 Å2-0.0203 Å2-0.0136 Å2-0.0145 Å2--0.0361 Å2
L0.2611 °20.0426 °2-0.0659 °2-0.1137 °2-0.0625 °2--0.1868 °2
S0.0627 Å °-0 Å °0.0371 Å °0.0081 Å °-0.0428 Å °0.035 Å °-0.0193 Å °0.0259 Å °0.0066 Å °
Refinement TLS groupSelection details: all

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