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- PDB-5jmn: Fusidic acid bound AcrB -

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Basic information

Entry
Database: PDB / ID: 5jmn
TitleFusidic acid bound AcrB
Components
  • DARPin
  • Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / Multidrug efflux protein / Membrane protein
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / outer membrane-bounded periplasmic space / 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 / 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
DECANE / DODECANE / Chem-ETE / FUSIDIC ACID / HEXANE / N-OCTANE / 3,6,9,12,15-PENTAOXAHEPTADECANE / PHOSPHATIDYLETHANOLAMINE / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOswald, C. / Tam, 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: Nat Commun / Year: 2016
Title: Transport of lipophilic carboxylates is mediated by transmembrane helix 2 in multidrug transporter AcrB.
Authors: Oswald, C. / Tam, H.K. / Pos, K.M.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Jan 10, 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)393,60746
Polymers380,8445
Non-polymers12,76341
Water14,682815
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44600 Å2
ΔGint-88 kcal/mol
Surface area125520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.654, 163.248, 246.042
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: 114736.289 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: acrB, acrE, b0462, JW0451 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (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) / Gene: Artificial gene / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue

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Sugars , 1 types, 10 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 11 types, 846 molecules

#3: Chemical ChemComp-FUA / FUSIDIC ACID


Mass: 516.709 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H48O6 / Comment: antibiotic, Antimicrobial*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H20O5
#8: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14
#9: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#10: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26
#11: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#12: Chemical ChemComp-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE


Mass: 250.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O5
#13: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 815 / 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: 3.84 Å3/Da / Density % sol: 67.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.05M ADA, pH 6.9, 0.15-0.25M AMMONIUM SULFATE, 5% GLYCEROL, 5-10% PEG4000, 0.004m FUSIDIC ACID

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.15 Å / Num. obs: 259156 / % possible obs: 92.8 % / Redundancy: 6.7 % / Net I/σ(I): 4.1
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DX7

4dx7


Resolution: 2.5→49.15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.905 / SU B: 13.8 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26147 10113 5 %RANDOM
Rwork0.22486 ---
obs0.22668 192130 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.517 Å2
Baniso -1Baniso -2Baniso -3
1--4.15 Å2-0 Å20 Å2
2--4.55 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 2.5→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25920 0 874 815 27609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01927306
X-RAY DIFFRACTIONr_bond_other_d0.0010.0227131
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.99636971
X-RAY DIFFRACTIONr_angle_other_deg0.838362427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.02553418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01824.6881056
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.779154445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.66715120
X-RAY DIFFRACTIONr_chiral_restr0.0590.24368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02130139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025847
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_it1.5126.16913657
X-RAY DIFFRACTIONr_mcbond_other1.5126.16913656
X-RAY DIFFRACTIONr_mcangle_it2.6369.25217065
X-RAY DIFFRACTIONr_mcangle_other2.6369.25217066
X-RAY DIFFRACTIONr_scbond_it1.4226.63213649
X-RAY DIFFRACTIONr_scbond_other1.4226.63213650
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5399.82719902
X-RAY DIFFRACTIONr_long_range_B_refined4.81849.43829766
X-RAY DIFFRACTIONr_long_range_B_other4.81749.43929767
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 740 -
Rwork0.394 14058 -
obs--99.93 %

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