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- PDB-5ent: Minocycline bound structure of bacterial efflux pump. -

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Basic information

Entry
Database: PDB / ID: 5ent
TitleMinocycline 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


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 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 ...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 / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MIY / DI(HYDROXYETHYL)ETHER / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Apr 25, 2018Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.4Jan 10, 2024Group: 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,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)252,7388
Polymers252,1756
Non-polymers5642
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24190 Å2
ΔGint-74 kcal/mol
Surface area85860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.557, 145.409, 175.612
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-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
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH6.5, 0.21 M NaCl, 11.5% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 96991 / % possible obs: 99.3 % / Redundancy: 9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.162 / Net I/σ(I): 11.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.241 / CC1/2: 0.617 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EN5

5en5


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.871 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24768 4767 4.9 %RANDOM
Rwork0.19337 ---
obs0.19601 92224 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.249 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å2-0 Å2-0 Å2
2---2.88 Å20 Å2
3---1.45 Å2
Refinement stepCycle: 1 / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16886 0 40 371 17297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01917222
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216400
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.95523357
X-RAY DIFFRACTIONr_angle_other_deg0.998337677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6252206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00825.635788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.863152872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4751572
X-RAY DIFFRACTIONr_chiral_restr0.0870.22645
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219961
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023835
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_it3.9635.048860
X-RAY DIFFRACTIONr_mcbond_other3.9495.0398859
X-RAY DIFFRACTIONr_mcangle_it6.0777.53911054
X-RAY DIFFRACTIONr_mcangle_other6.0787.5411055
X-RAY DIFFRACTIONr_scbond_it4.2485.4548362
X-RAY DIFFRACTIONr_scbond_other4.2485.4548363
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7247.99912304
X-RAY DIFFRACTIONr_long_range_B_refined9.14539.26918587
X-RAY DIFFRACTIONr_long_range_B_other9.1539.30318463
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.504→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 346 -
Rwork0.342 6655 -
obs--98.88 %

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