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Yorodumi- PDB-2hqd: Conformation of the AcrB Multidrug Efflux Pump in Mutants of the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hqd | ||||||
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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 / efflux transmembrane transporter activity / xenobiotic 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: 3.65 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 | 2hqd.cif.gz | 205.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hqd.ent.gz | 162.4 KB | Display | PDB format |
PDBx/mmJSON format | 2hqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hqd_validation.pdf.gz | 414.6 KB | Display | wwPDB validaton report |
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Full document | 2hqd_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 2hqd_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 2hqd_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/2hqd ftp://data.pdbj.org/pub/pdb/validation_reports/hq/2hqd | HTTPS FTP |
-Related structure data
Related structure data | 2hqcC 2hqfC 2hqgC 1t9uS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 114173.742 Da / Num. of mol.: 1 / Mutation: D408A 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: 4.57 Å3/Da / Density % sol: 73.11 % |
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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: 3.65→50 Å / Num. obs: 585851 / % possible obs: 94.7 % / Observed criterion σ(I): 1.3 |
Reflection shell | Resolution: 3.65→3.78 Å / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T9U Resolution: 3.65→20 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.864 / SU B: 28.622 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.725 / 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: 100.25 Å2
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Refinement step | Cycle: LAST / Resolution: 3.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.65→3.74 Å / Total num. of bins used: 20
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