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- PDB-7ouk: BDM88855 inhibitor bound to the transmembrane domain of AcrB -

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Basic information

Entry
Database: PDB / ID: 7ouk
TitleBDM88855 inhibitor bound to the transmembrane domain of AcrB
Components
  • DARPIN
  • Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / Multidrug efflux pump / Membrane 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 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-chloranyl-2-piperazin-1-yl-quinoline / TETRADECANE / DECANE / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / (2S)-3-hydroxypropane-1,2-diyl didecanoate / Chem-LPX / N-OCTANE / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTam, H.K. / Foong, W.E. / Pos, K.M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 807, Transport and Communication across Biological Membranes Germany
CitationJournal: Nat Commun / Year: 2022
Title: Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps.
Authors: Ple, C. / Tam, H.K. / Vieira Da Cruz, A. / Compagne, N. / Jimenez-Castellanos, J.C. / Muller, R.T. / Pradel, E. / Foong, W.E. / Malloci, G. / Ballee, A. / Kirchner, M.A. / Moshfegh, P. / ...Authors: Ple, C. / Tam, H.K. / Vieira Da Cruz, A. / Compagne, N. / Jimenez-Castellanos, J.C. / Muller, R.T. / Pradel, E. / Foong, W.E. / Malloci, G. / Ballee, A. / Kirchner, M.A. / Moshfegh, P. / Herledan, A. / Herrmann, A. / Deprez, B. / Willand, N. / Vargiu, A.V. / Pos, K.M. / Flipo, M. / Hartkoorn, R.C.
History
DepositionJun 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)389,72349
Polymers380,8445
Non-polymers8,87944
Water6,575365
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40350 Å2
ΔGint-75 kcal/mol
Surface area123290 Å2
Unit cell
Length a, b, c (Å)146.126, 159.647, 245.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 (E. coli) / Strain: K12 / Gene: acrB, acrE, b0462, JW0451 / Plasmid: PET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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 K-12 (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, 401 molecules

#4: Chemical ChemComp-1K8 / 3-chloranyl-2-piperazin-1-yl-quinoline / BDM88855 / 153987774


Mass: 247.723 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14ClN3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18
#7: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H30
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#10: 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
#11: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27NO
#12: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#13: Chemical ChemComp-LPX / (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate


Mass: 453.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H44NO7P
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 3.87 Å3/Da / Density % sol: 68.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.05M ADA, PH 6.6, 0.13-0.2M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000, 0.008M BDM88855

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.6→49.1 Å / Num. obs: 176116 / % possible obs: 99.9 % / Redundancy: 13.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.063 / Rrim(I) all: 0.235 / Net I/σ(I): 9.5 / Num. measured all: 2454422 / Scaling rejects: 296
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.64142.08112081286110.5970.5722.1581.799.7
14.24-49.111.40.051362911930.9990.0170.05327.497.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
REFMAC5.8.0258phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JMN

5jmn


Resolution: 2.6→49.05 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.904 / SU B: 26.307 / SU ML: 0.257 / SU R Cruickshank DPI: 0.4212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.421 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 8846 5 %RANDOM
Rwork0.2365 ---
obs0.2377 167178 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 max: 145.77 Å2 / Biso mean: 55.257 Å2 / Biso min: 23.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å20 Å2
2--0.3 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 2.6→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25930 0 599 365 26894
Biso mean--71.86 39.92 -
Num. residues----3411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01327040
X-RAY DIFFRACTIONr_bond_other_d0.0010.01726097
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.64936620
X-RAY DIFFRACTIONr_angle_other_deg1.0221.58660453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.77253415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.62223.1221182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.408154456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.78915123
X-RAY DIFFRACTIONr_chiral_restr0.0310.23647
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0229671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025340
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 699 -
Rwork0.33 12122 -
all-12821 -
obs--99.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59060.0507-0.10750.2477-0.2640.94370.07970.03870.32220.1606-0.01960.0237-0.4679-0.0409-0.06010.23840.030.04230.4903-0.01790.179229.994-14.254-17.061
20.20790.00490.03560.3003-0.31270.46540.02720.2313-0.0218-0.17850.02170.09540.1566-0.079-0.04890.1250.0291-0.05910.5994-0.01910.143929.033-40.929-52.755
30.46210.1097-0.10450.2195-0.16280.60030.03190.08430.0495-0.0182-0.00880.0104-0.0620.0335-0.02320.01740.01180.00210.39150.00410.028367.715-25.835-35.149
42.8719-0.18731.87921.89350.61735.2538-0.0941-0.00150.11030.0644-0.02550.1736-0.2371-0.3140.11970.0606-0.0967-0.00510.3776-0.10170.22250.786-73.957-23.504
53.1137-1.5314-0.4694.280.482.27480.0453-0.50760.42660.2908-0.0022-0.3831-0.32870.1884-0.04310.217-0.1197-0.03490.6327-0.06290.071346.89-37.87328.133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1042
2X-RAY DIFFRACTION1A1101 - 1110
3X-RAY DIFFRACTION1B1501 - 1502
4X-RAY DIFFRACTION1C1701 - 1702
5X-RAY DIFFRACTION2B1 - 1036
6X-RAY DIFFRACTION2B1503 - 1515
7X-RAY DIFFRACTION3C1 - 1033
8X-RAY DIFFRACTION3A1111 - 1112
9X-RAY DIFFRACTION3B1516
10X-RAY DIFFRACTION3C1703 - 1712
11X-RAY DIFFRACTION4D12 - 167
12X-RAY DIFFRACTION5E14 - 166
13X-RAY DIFFRACTION5A1113

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