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- PDB-7oum: BDM88855 inhibitor bound to the transmembrane domain of AcrB-R971A -

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Basic information

Entry
Database: PDB / ID: 7oum
TitleBDM88855 inhibitor bound to the transmembrane domain of AcrB-R971A
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 / 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: 2.45 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)388,26048
Polymers380,5865
Non-polymers7,67443
Water12,088671
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39690 Å2
ΔGint-9 kcal/mol
Surface area122870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.214, 161.631, 244.437
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: 114650.180 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, 7 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 10 types, 707 molecules

#4: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30
#5: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: 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
#8: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#11: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18
#12: Chemical ChemComp-LPX / (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate


Mass: 453.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44NO7P
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.9 Å3/Da / Density % sol: 68.51 %
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, 0.006M BDM88855

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.45→49.51 Å / Num. obs: 212143 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.281 / Rpim(I) all: 0.078 / Rrim(I) all: 0.292 / Net I/σ(I): 6.5 / Num. measured all: 2939346 / Scaling rejects: 1264
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
2.45-2.49142.05145428103840.5930.5652.1271.5100
13.42-49.5111.70.1071676714300.9990.0370.11414.298.1

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Processing

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

5jmn


Resolution: 2.45→49.51 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.2547 / WRfactor Rwork: 0.2268 / FOM work R set: 0.7838 / SU B: 19.349 / SU ML: 0.212 / SU R Cruickshank DPI: 0.3068 / SU Rfree: 0.2336 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.307 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 10468 4.9 %RANDOM
Rwork0.228 ---
obs0.2294 201567 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.83 Å2 / Biso mean: 49.147 Å2 / Biso min: 20.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.07 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 2.45→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25894 0 519 671 27084
Biso mean--63.89 38.03 -
Num. residues----3410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01326931
X-RAY DIFFRACTIONr_bond_other_d0.0010.01725974
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.64736484
X-RAY DIFFRACTIONr_angle_other_deg1.0331.58360152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.90253414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.60423.2031177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.407154440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.28815120
X-RAY DIFFRACTIONr_chiral_restr0.0320.23633
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0229642
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025324
LS refinement shellResolution: 2.45→2.513 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 732 -
Rwork0.312 14766 -
all-15498 -
obs--100 %
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)
10.47730.1002-0.10660.4475-0.20780.81310.06620.04160.26830.13650.02490.0322-0.3885-0.0457-0.09110.19090.02840.06120.36920.0030.25830.102-14.53-16.89
20.2373-0.04790.01260.2744-0.2490.36990.03920.22640.0165-0.1909-0.0140.08450.1391-0.0964-0.02520.14350.0133-0.060.48570.00730.282829.092-41.417-52.559
30.43180.1332-0.11290.3148-0.16520.57810.02430.06360.0538-0.0153-0.0115-0.0009-0.06760.0559-0.01280.01410.00220.0030.29610.01810.146767.915-26.096-34.797
42.8097-0.3161.72081.59170.41444.6429-0.0709-0.09830.00410.0309-0.05230.1851-0.2475-0.3690.12320.0855-0.11230.00650.2925-0.08460.29481.064-74.497-23.899
53.0804-0.9879-0.44843.52530.53592.26290.0212-0.56510.44520.35850.047-0.3839-0.31640.143-0.06820.2625-0.0883-0.03230.6546-0.07660.180746.912-38.5328.101
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1041
2X-RAY DIFFRACTION1A1101 - 1111
3X-RAY DIFFRACTION2B1 - 1034
4X-RAY DIFFRACTION2A1112
5X-RAY DIFFRACTION2B1101 - 1112
6X-RAY DIFFRACTION3C1 - 1033
7X-RAY DIFFRACTION3B1113
8X-RAY DIFFRACTION3C1101 - 1114
9X-RAY DIFFRACTION4D12 - 166
10X-RAY DIFFRACTION4D201
11X-RAY DIFFRACTION5E13 - 166
12X-RAY DIFFRACTION5E201

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