+Open data
-Basic information
Entry | Database: PDB / ID: 7ouk | ||||||
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Title | BDM88855 inhibitor bound to the transmembrane domain of AcrB | ||||||
Components |
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Keywords | TRANSPORT 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 / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / outer membrane-bounded periplasmic space / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Tam, H.K. / Foong, W.E. / Pos, K.M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ouk.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ouk.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7ouk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ouk_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 7ouk_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 7ouk_validation.xml.gz | 114.1 KB | Display | |
Data in CIF | 7ouk_validation.cif.gz | 155.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/7ouk ftp://data.pdbj.org/pub/pdb/validation_reports/ou/7ouk | HTTPS FTP |
-Related structure data
Related structure data | 7oulC 7oumC 5jmnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 5 molecules ABCDE
#1: Protein | 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 | 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 / |
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-Non-polymers , 11 types, 401 molecules
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-GOL / #9: Chemical | ChemComp-D10 / | #10: Chemical | ChemComp-DDR / ( | #11: Chemical | ChemComp-DDQ / | #12: Chemical | #13: Chemical | #14: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.23 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 14, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.77 Å2 / Biso mean: 55.257 Å2 / Biso min: 23.74 Å2
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Refinement step | Cycle: final / Resolution: 2.6→49.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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