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- PDB-5enq: MBX3132 bound structure of bacterial efflux pump. -

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Basic information

Entry
Database: PDB / ID: 5enq
TitleMBX3132 bound structure of bacterial efflux pump.
Components
  • DARPin
  • Multidrug efflux pump subunit AcrB,Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / Efflux pump
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 pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / 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 ...Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / 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 / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5QE / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSjuts, H. / Ornik, A.R. / Pos, K.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives.
Authors: Sjuts, H. / Vargiu, A.V. / Kwasny, S.M. / Nguyen, S.T. / Kim, H.S. / Ding, X. / Ornik, A.R. / Ruggerone, P. / Bowlin, T.L. / Nikaido, H. / Pos, K.M. / Opperman, T.J.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Jan 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)252,6697
Polymers252,1756
Non-polymers4951
Water24,4101355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22910 Å2
ΔGint-64 kcal/mol
Surface area85180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.726, 145.517, 173.452
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,Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 65740.656 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224
#2: Protein DARPin


Mass: 18317.566 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: Ribosome display vector pRDV / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-5QE / ~{N}-[4-[2-[[5-cyano-8-[(2~{S},6~{R})-2,6-dimethylmorpholin-4-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridin-6-yl]sulfanyl]ethyl]phenyl]ethanamide


Mass: 494.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H34N4O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1355 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 MES pH6.5, 0.21 M NaCl, 11.5% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 251472 / % possible obs: 99.8 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Net I/σ(I): 12.96
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.949 / CC1/2: 0.484 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EN5

5en5


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.376 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22291 12408 4.9 %RANDOM
Rwork0.18186 ---
obs0.18387 238859 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.829 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å2-0 Å2
2---0.69 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16867 0 35 1355 18257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01917209
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216387
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.95423339
X-RAY DIFFRACTIONr_angle_other_deg1.022337650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16652207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35325.627789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.497152871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1581572
X-RAY DIFFRACTIONr_chiral_restr0.1140.22640
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219945
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023835
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_it3.273.3888852
X-RAY DIFFRACTIONr_mcbond_other3.273.3888851
X-RAY DIFFRACTIONr_mcangle_it4.5025.05911045
X-RAY DIFFRACTIONr_mcangle_other4.5025.0611046
X-RAY DIFFRACTIONr_scbond_it4.4813.8958357
X-RAY DIFFRACTIONr_scbond_other4.4813.8968358
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.815.63112293
X-RAY DIFFRACTIONr_long_range_B_refined8.52927.93320113
X-RAY DIFFRACTIONr_long_range_B_other8.47627.62419393
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 927 -
Rwork0.333 17424 -
obs--99.79 %

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