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Yorodumi- PDB-2dr6: Crystal structure of a multidrug transporter reveal a functionall... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dr6 | ||||||
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Title | Crystal structure of a multidrug transporter reveal a functionally rotating mechanism | ||||||
Components | ACRBAcriflavine resistance protein family | ||||||
Keywords | MEMBRANE PROTEIN / membrane transporter / multidrug efflux / drug resistance / transporter / exporter / antiporter | ||||||
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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 3.3 Å | ||||||
Authors | Murakami, S. / Nakashima, R. / Yamashita, E. / Matsumoto, T. | ||||||
Citation | Journal: Nature / Year: 2006 Title: Crystal structures of a multidrug transporter reveal a functionally rotating mechanism Authors: Murakami, S. / Nakashima, R. / Yamashita, E. / Matsumoto, T. / Yamaguchi, A. | ||||||
History |
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Remark 650 | HELIX determination method: Author determined. | ||||||
Remark 700 | SHEET determination method: Author determined. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dr6.cif.gz | 603.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dr6.ent.gz | 472.2 KB | Display | PDB format |
PDBx/mmJSON format | 2dr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/2dr6 ftp://data.pdbj.org/pub/pdb/validation_reports/dr/2dr6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 114217.742 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PUC-118 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P31224 #2: Chemical | ChemComp-DM2 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.52 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.1 / Details: PEG4000, PH 6.1, VAPOR DIFFUSION, SITTING DROP |
-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: MACSCIENCE / Detector: IMAGE PLATE / Date: Apr 4, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 69300 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 1.8 / % possible all: 84.2 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 3.3→10 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.832 / SU B: 35.125 / SU ML: 0.589 / Cross valid method: THROUGHOUT / ESU R Free: 0.755 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 116.594 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.38 Å / Total num. of bins used: 20
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