[English] 日本語
Yorodumi- PDB-1oyd: Structural Basis of Multiple Binding Capacity of the AcrB multidr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oyd | ||||||
---|---|---|---|---|---|---|---|
Title | Structural Basis of Multiple Binding Capacity of the AcrB multidrug Efflux Pump | ||||||
Components | Acriflavine resistance protein B | ||||||
Keywords | 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Yu, E.W. / MeDermott, G. / Zgurskaya, H.I. / Nikaido, H. / Koshland Jr., D.E. | ||||||
Citation | Journal: Science / Year: 2003 Title: Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump. Authors: Yu, E.W. / McDermott, G. / Zgurskaya, H.I. / Nikaido, H. / Koshland, D.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1oyd.cif.gz | 203.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1oyd.ent.gz | 160.1 KB | Display | PDB format |
PDBx/mmJSON format | 1oyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/1oyd ftp://data.pdbj.org/pub/pdb/validation_reports/oy/1oyd | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 113665.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ACRB OR ACRE OR B0462 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224 |
---|---|
#2: Chemical | ChemComp-DEQ / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.86 Å3/Da / Density % sol: 74.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 5.6 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.78→46.61 Å / Num. all: 21326 / Num. obs: 21326 / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 3.8 Å / Num. obs: 35008 / % possible obs: 98 % / Num. measured all: 212408 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS Highest resolution: 3.8 Å / Lowest resolution: 3.94 Å / % possible obs: 99.3 % / Rmerge(I) obs: 0.538 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→46.6 Å / σ(F): 0
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→46.6 Å
| ||||||||||||||||||||
Software | *PLUS Version: 5 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 46.6 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |