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- PDB-6q4o: Fusidic acid bound AcrB_I27A -

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Basic information

Entry
Database: PDB / ID: 6q4o
TitleFusidic acid bound AcrB_I27A
Components
  • DARPIN
  • Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / Multidrug efflux protein / Membrane 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 TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 2-Layer Sandwich ...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 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DECANE / DODECANE / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / (2S)-3-hydroxypropane-1,2-diyl didecanoate / FUSIDIC ACID / HEXANE / N-OCTANE / PHOSPHATIDYLETHANOLAMINE / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTam, H.K. / Pos, K.M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB807 (Transport and Communication across Biological Membranes Germany
German Research FoundationDFG EXC115 (Cluster of Excellence Frankfurt Macromolecular Complexes) Germany
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB.
Authors: Tam, H.K. / Malviya, V.N. / Foong, W.E. / Herrmann, A. / Malloci, G. / Ruggerone, P. / Vargiu, A.V. / Pos, K.M.
History
DepositionDec 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)394,62965
Polymers380,7185
Non-polymers13,91260
Water11,530640
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53420 Å2
ΔGint59 kcal/mol
Surface area121420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.203, 162.571, 243.459
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 5 molecules ABCDE

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


Mass: 114694.211 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 / Gene: acrB, acrE, b0462, JW0451 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 (DE3) / 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) / Gene: artificial gene / Plasmid: pQE30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): XL1 Blue

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Sugars , 1 types, 8 molecules

#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 11 types, 692 molecules

#4: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H22
#5: Chemical
ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C12H27NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14
#8: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18
#9: Chemical ChemComp-FUA / FUSIDIC ACID


Mass: 516.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H48O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, Antimicrobial*YM
#10: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26
#11: Chemical ChemComp-DDR / (2S)-3-hydroxypropane-1,2-diyl didecanoate / 1,2-DIDECANOYL-SN-GLYCEROL


Mass: 400.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O5
#12: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#13: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

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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: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.05M ADA, PH 6.6, 0.15-0.25M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→48.4 Å / Num. obs: 140232 / % possible obs: 99.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.193 / Net I/σ(I): 8.2
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 1.363

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JMN

5jmn


Resolution: 2.8→47.52 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.873 / SU B: 15.239 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.668 / ESU R Free: 0.333 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25557 6961 5 %RANDOM
Rwork0.21179 ---
obs0.21397 133220 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.537 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å2-0 Å20 Å2
2--2.12 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25988 0 956 643 27587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01327445
X-RAY DIFFRACTIONr_bond_other_d0.0010.01726867
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.65737080
X-RAY DIFFRACTIONr_angle_other_deg1.091.60462291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91253428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59223.1041192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.216154458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.80715123
X-RAY DIFFRACTIONr_chiral_restr0.0430.23675
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0229784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025353
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2274.9313691
X-RAY DIFFRACTIONr_mcbond_other1.2274.9313690
X-RAY DIFFRACTIONr_mcangle_it2.1697.39417108
X-RAY DIFFRACTIONr_mcangle_other2.1697.39417109
X-RAY DIFFRACTIONr_scbond_it1.1575.29713754
X-RAY DIFFRACTIONr_scbond_other1.1575.29713755
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0597.81719967
X-RAY DIFFRACTIONr_long_range_B_refined5.70893.731110619
X-RAY DIFFRACTIONr_long_range_B_other5.70893.732110620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 516 -
Rwork0.334 9822 -
obs--99.71 %

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