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Yorodumi- PDB-3w9j: Structural basis for the inhibition of bacterial multidrug exporters -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w9j | ||||||
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Title | Structural basis for the inhibition of bacterial multidrug exporters | ||||||
Components | Multidrug resistance protein MexBMultiple drug resistance | ||||||
Keywords | MEMBRANE PROTEIN / MexB / Efflux pump / Transporter / Multidrug efflux pump / MexA / OprM / Inner Membrane / Transport protein | ||||||
Function / homology | Function and homology information xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / transmembrane transport / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 Å | ||||||
Authors | Sakurai, K. / Nakashima, R. / Hayashi, K. / Yamaguchi, A. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Structural basis for the inhibition of bacterial multidrug exporters Authors: Nakashima, R. / Sakurai, K. / Yamasaki, S. / Hayashi, K. / Nagata, C. / Hoshino, K. / Onodera, Y. / Nishino, K. / Yamaguchi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w9j.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3w9j.ent.gz | 954.9 KB | Display | PDB format |
PDBx/mmJSON format | 3w9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/3w9j ftp://data.pdbj.org/pub/pdb/validation_reports/w9/3w9j | HTTPS FTP |
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-Related structure data
Related structure data | 3w9hC 3w9iC 2v50S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / Refine code: 4
NCS ensembles :
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-Components
#1: Protein | Mass: 113706.008 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: mexB, PA0426 / Plasmid: pUCP20 / Production host: Escherichia coli (E. coli) / Strain (production host): MG1655 / References: UniProt: P52002 #2: Sugar | ChemComp-LMT / #3: Chemical | |
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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: 3.59 Å3/Da / Density % sol: 65.75 % / Mosaicity: 0.918 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 50mM Na Acetate-HCl pH5.0, 300mM NaCl, 25% PEG400, 32ug/ml ABI-PP, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 27, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.15→100 Å / Num. obs: 160614 / % possible obs: 98.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.091 / Χ2: 1.705 / Net I/σ(I): 10.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V50 Resolution: 3.15→42.19 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.2602 / WRfactor Rwork: 0.1881 / Occupancy max: 1 / Occupancy min: 0.6 / FOM work R set: 0.7664 / SU B: 22.884 / SU ML: 0.388 / SU Rfree: 0.5043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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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: 291.27 Å2 / Biso mean: 83.2169 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 3.15→42.19 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.152→3.233 Å / Total num. of bins used: 20
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