[English] 日本語
![](img/lk-miru.gif)
- PDB-6zog: Minocycline binding to the deep binding pocket of AcrB-I38F_I671T -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6zog | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Minocycline binding to the deep binding pocket of AcrB-I38F_I671T | ||||||||||||
![]() |
| ||||||||||||
![]() | TRANSPORT PROTEIN / Multidrug efflux pump / Membrane protein | ||||||||||||
Function / homology | ![]() 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Tam, H.K. / Foong, W.E. / Pos, K.M. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Allosteric drug transport mechanism of multidrug transporter AcrB. Authors: Tam, H.K. / Foong, W.E. / Oswald, C. / Herrmann, A. / Zeng, H. / Pos, K.M. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 664.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 531.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 110.4 KB | Display | |
Data in CIF | ![]() | 148.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zo5C ![]() 6zo6C ![]() 6zo7C ![]() 6zo8C ![]() 6zo9C ![]() 6zoaC ![]() 6zobC ![]() 6zocC ![]() 6zodC ![]() 6zoeC ![]() 6zofC ![]() 6zohC ![]() 5jmnS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 5 molecules ABCDE
#1: Protein | Mass: 114758.258 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 18317.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: ARTIFICIAL GENE / Plasmid: PQE30 / Production host: ![]() ![]() |
---|
-Sugars , 1 types, 6 molecules ![](data/chem/img/LMT.gif)
#3: Sugar | ChemComp-LMT / |
---|
-Non-polymers , 14 types, 158 molecules ![](data/chem/img/D10.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DDR.gif)
![](data/chem/img/MYS.gif)
![](data/chem/img/8K6.gif)
![](data/chem/img/MIY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/OCT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/D12.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/C14.gif)
![](data/chem/img/DDQ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DDR.gif)
![](data/chem/img/MYS.gif)
![](data/chem/img/8K6.gif)
![](data/chem/img/MIY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/OCT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/D12.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/C14.gif)
![](data/chem/img/DDQ.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-DDR / ( | #7: Chemical | ChemComp-MYS / | #8: Chemical | ChemComp-8K6 / | #9: Chemical | ChemComp-MIY / ( | #10: Chemical | ChemComp-GOL / #11: Chemical | ChemComp-OCT / | #12: Chemical | #13: Chemical | ChemComp-D12 / | #14: Chemical | ChemComp-PTY / | #15: Chemical | ChemComp-C14 / | #16: Chemical | ChemComp-DDQ / | #17: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.53 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.05M ADA, PH 6.6, 0.15-0.25M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000, 0.002M MINOCYCLINE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2016 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.75→49.59 Å / Num. obs: 151127 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.074 / Rrim(I) all: 0.205 / Net I/σ(I): 9.8 / Num. measured all: 1141557 / Scaling rejects: 256 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5JMN Resolution: 2.75→49.59 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.882 / SU B: 18.141 / SU ML: 0.321 / SU R Cruickshank DPI: 0.5452 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.545 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 151.54 Å2 / Biso mean: 61.673 Å2 / Biso min: 26 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→49.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|