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- PDB-4u8y: Coupling of remote alternating-access transport mechanisms for pr... -

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Basic information

Entry
Database: PDB / ID: 4u8y
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: 2.099 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. / Brandstatter, 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)383,34110
Polymers380,8415
Non-polymers2,5005
Water38,0302111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26340 Å2
ΔGint-86 kcal/mol
Surface area123120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.880, 161.160, 245.290
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: 114735.305 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: acrB, acrE, b0462, JW0451 / 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) / 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.: 4 / 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: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2111 / 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: 3.79 Å3/Da / Density % sol: 67.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M ADA, pH 6.5, 0.2 M (NH4)2SO4, 7% PEG4000, 8% 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: 2.099→48.8 Å / Num. obs: 332174 / % possible obs: 99.16 % / Redundancy: 7.2 % / Net I/σ(I): 9.63
Reflection shellResolution: 2.099→2.174 Å / Redundancy: 5 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 0.78 / % possible all: 92.75

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DX5

4dx5


Resolution: 2.099→48.799 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2363 16610 5 %
Rwork0.193 --
obs0.1952 332135 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.099→48.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25969 0 161 2111 28241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826630
X-RAY DIFFRACTIONf_angle_d1.03936174
X-RAY DIFFRACTIONf_dihedral_angle_d15.1069669
X-RAY DIFFRACTIONf_chiral_restr0.0424267
X-RAY DIFFRACTIONf_plane_restr0.0054623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0994-2.12320.38524980.3649455X-RAY DIFFRACTION90
2.1232-2.14820.38785140.35429784X-RAY DIFFRACTION93
2.1482-2.17440.33775290.333310032X-RAY DIFFRACTION95
2.1744-2.20190.36235380.3210218X-RAY DIFFRACTION97
2.2019-2.23090.31625520.304610491X-RAY DIFFRACTION99
2.2309-2.26150.3385560.281910548X-RAY DIFFRACTION100
2.2615-2.29380.31385520.260810497X-RAY DIFFRACTION100
2.2938-2.3280.29185550.253310555X-RAY DIFFRACTION100
2.328-2.36440.30515560.253610537X-RAY DIFFRACTION100
2.3644-2.40320.28485540.232310539X-RAY DIFFRACTION100
2.4032-2.44460.27015560.225610569X-RAY DIFFRACTION100
2.4446-2.48910.26715540.213810508X-RAY DIFFRACTION100
2.4891-2.53690.2695550.214210546X-RAY DIFFRACTION100
2.5369-2.58870.26295560.21110580X-RAY DIFFRACTION100
2.5887-2.6450.25045590.202710598X-RAY DIFFRACTION100
2.645-2.70650.24525540.196510523X-RAY DIFFRACTION100
2.7065-2.77420.24815580.19210599X-RAY DIFFRACTION100
2.7742-2.84920.23365560.182610578X-RAY DIFFRACTION100
2.8492-2.9330.23295580.181110589X-RAY DIFFRACTION100
2.933-3.02770.23495570.182410594X-RAY DIFFRACTION100
3.0277-3.13590.23595570.176310573X-RAY DIFFRACTION100
3.1359-3.26140.21475590.170210624X-RAY DIFFRACTION100
3.2614-3.40980.22995600.17110632X-RAY DIFFRACTION100
3.4098-3.58950.21825600.163710631X-RAY DIFFRACTION100
3.5895-3.81430.1835620.154710674X-RAY DIFFRACTION100
3.8143-4.10870.19595610.156410666X-RAY DIFFRACTION100
4.1087-4.52190.18525640.152610713X-RAY DIFFRACTION100
4.5219-5.17560.18275660.149210759X-RAY DIFFRACTION100
5.1756-6.51830.22565700.176110826X-RAY DIFFRACTION100
6.5183-48.8120.21515840.175111087X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 40.5899 Å / Origin y: -31.2748 Å / Origin z: -30.4109 Å
111213212223313233
T0.1637 Å20.0175 Å2-0.0139 Å2-0.1345 Å2-0.0035 Å2--0.1516 Å2
L0.4206 °20.0636 °2-0.1003 °2-0.1971 °2-0.082 °2--0.3177 °2
S0.0479 Å °0.0668 Å °0.0563 Å °-0.0037 Å °-0.0265 Å °0.0407 Å °-0.0488 Å °-0.0432 Å °-0.0045 Å °
Refinement TLS groupSelection details: all

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