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- PDB-7oul: BDM88832 inhibitor bound to the transmembrane domain of AcrB-R971A -

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Basic information

Entry
Database: PDB / ID: 7oul
TitleBDM88832 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


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / outer membrane-bounded periplasmic space / membrane / identical protein binding / plasma membrane
Similarity search - Function
Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
1-(3-chloranyl-5-iodanyl-pyridin-2-yl)piperazine / TETRADECANE / DODECANE / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / Chem-LPX / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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)386,15232
Polymers380,5865
Non-polymers5,56627
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33950 Å2
ΔGint-82 kcal/mol
Surface area123300 Å2
Unit cell
Length a, b, c (Å)146.408, 160.012, 245.478
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, 6 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 9 types, 194 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-1KE / 1-(3-chloranyl-5-iodanyl-pyridin-2-yl)piperazine / BDM88832


Mass: 323.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11ClIN3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: 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
#10: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27NO
#11: Chemical ChemComp-C14 / TETRADECANE / Tetradecane


Mass: 198.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.89 Å3/Da / Density % sol: 68.37 %
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 BDM88832

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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: 2.8→49.43 Å / Num. obs: 142096 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.275 / Rpim(I) all: 0.076 / Rrim(I) all: 0.285 / Net I/σ(I): 9.3 / Num. measured all: 1975241 / Scaling rejects: 226
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
2.8-2.8514.32.0589918169380.6030.5622.1341.6100
15.34-49.4311.50.046111149690.9990.0160.04930.997.3

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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: 2.8→49.43 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.887 / SU B: 35.883 / SU ML: 0.312 / SU R Cruickshank DPI: 0.6554 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.655 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 6989 4.9 %RANDOM
Rwork0.2422 ---
obs0.2431 135011 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.27 Å2 / Biso mean: 57.192 Å2 / Biso min: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å2-0 Å20 Å2
2--1.48 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 2.8→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25882 0 365 173 26420
Biso mean--73.06 34.89 -
Num. residues----3408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01326739
X-RAY DIFFRACTIONr_bond_other_d0.0010.01725667
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.64236267
X-RAY DIFFRACTIONr_angle_other_deg1.0261.5859429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.69453406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1423.2341172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.084154425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.78715118
X-RAY DIFFRACTIONr_chiral_restr0.0310.23618
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0229553
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025300
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 520 -
Rwork0.338 9832 -
all-10352 -
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)
10.60970.0899-0.09970.5396-0.30780.82940.07950.02640.3260.1709-0.00730.0146-0.4234-0.0438-0.07220.21790.0280.05070.3959-0.00820.180330.108-14.483-16.859
20.25720.0254-0.03580.3098-0.2380.36560.0240.29430.0121-0.22540.01330.07860.1505-0.0991-0.03730.17610.0244-0.05160.55150.00680.183929.131-41.439-52.492
30.56180.1155-0.1180.2184-0.14420.61180.02880.09220.0758-0.035-0.00290.0032-0.0460.037-0.02580.01960.00850.00190.290.00970.050767.919-26.1-34.856
42.9144-0.12081.76441.36660.41844.3913-0.1369-0.00510.08020.0684-0.09260.1667-0.2491-0.29510.22940.0877-0.1033-0.0130.2767-0.110.24120.948-74.075-23.915
52.4929-1.0042-0.55314.24160.62442.310.0641-0.50520.41810.3716-0.0112-0.3973-0.38890.1852-0.05290.223-0.1215-0.04310.6172-0.06220.088946.809-37.91828.124
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1042
2X-RAY DIFFRACTION1A1101 - 1106
3X-RAY DIFFRACTION1B1301
4X-RAY DIFFRACTION1C1601
5X-RAY DIFFRACTION2B1 - 1034
6X-RAY DIFFRACTION2B1302 - 1309
7X-RAY DIFFRACTION3C1 - 1033
8X-RAY DIFFRACTION3C1602 - 1607
9X-RAY DIFFRACTION4D12 - 166
10X-RAY DIFFRACTION4D201 - 202
11X-RAY DIFFRACTION5E13 - 166
12X-RAY DIFFRACTION5E201

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