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Yorodumi- PDB-2hqf: Conformation of the AcrB Multidrug Efflux Pump in Mutants of the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hqf | ||||||
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Title | Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway | ||||||
Components | Acriflavine resistance protein B | ||||||
Keywords | MEMBRANE PROTEIN / multidrug efflux pump | ||||||
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 K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å | ||||||
Authors | Su, C.-C. / Li, M. / Gu, R. / Takatsuka, Y. / McDermott, G. / Nikaido, H. / Yu, E.W. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2006 Title: Conformation of the AcrB multidrug efflux pump in mutants of the putative proton relay pathway Authors: Su, C.-C. / Li, M. / Gu, R. / Takatsuka, Y. / McDermott, G. / Nikaido, H. / Yu, E.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hqf.cif.gz | 204.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hqf.ent.gz | 162.1 KB | Display | PDB format |
PDBx/mmJSON format | 2hqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/2hqf ftp://data.pdbj.org/pub/pdb/validation_reports/hq/2hqf | 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: 114159.648 Da / Num. of mol.: 1 / Mutation: K940A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: acrB, acrE, b0462 / Plasmid: PSPORT1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) / References: UniProt: P31224 |
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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: 4.67 Å3/Da / Density % sol: 73.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9799 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2005 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 3.38→50 Å / Num. obs: 879227 / % possible obs: 99.9 % / Observed criterion σ(I): 1.4 |
Reflection shell | Resolution: 3.38→3.56 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.38→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.886 / SU B: 20.136 / SU ML: 0.339 / Cross valid method: THROUGHOUT / ESU R Free: 0.504 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.674 Å2
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Refinement step | Cycle: LAST / Resolution: 3.38→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.38→3.465 Å / Total num. of bins used: 20
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