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- PDB-6zob: 3-Formylrifamycin SV binding to the access pocket of AcrB L protomer -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zob | ||||||||||||
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Title | 3-Formylrifamycin SV binding to the access pocket of AcrB L protomer | ||||||||||||
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![]() | TRANSPORT PROTEIN / Multidrug efflux pump / Membrane protein | ||||||||||||
Function / homology | ![]() alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic transport ...alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / response to toxic substance / response to xenobiotic stimulus / response to antibiotic / 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 655.5 KB | Display | ![]() |
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PDB format | ![]() | 525.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 109.5 KB | Display | |
Data in CIF | ![]() | 148.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zo5C ![]() 6zo6C ![]() 6zo7C ![]() 6zo8C ![]() 6zo9C ![]() 6zoaC ![]() 6zocC ![]() 6zodC ![]() 6zoeC ![]() 6zofC ![]() 6zogC ![]() 6zohC ![]() 5jmnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 5 molecules ABCDE
#1: Protein | Mass: 114736.289 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#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 
#3: Sugar | ChemComp-LMT / |
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-Non-polymers , 11 types, 166 molecules 




















#4: Chemical | ChemComp-HEX / |
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#5: Chemical | ChemComp-GOL / |
#6: Chemical | ChemComp-ETE / |
#7: Chemical | ChemComp-3YI / ( |
#8: Chemical | ChemComp-EDO / |
#9: Chemical | ChemComp-DDR / ( |
#10: Chemical | ChemComp-DDQ / |
#11: Chemical | ChemComp-OCT / |
#12: Chemical | ChemComp-D10 / |
#13: Chemical | ChemComp-CL / |
#14: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.05M ADA, PH 6.9, 0.15-0.25M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000, 0.003M rifampicin |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.8→49.15 Å / Num. obs: 140616 / % possible obs: 100 % / Redundancy: 9.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.08 / Rrim(I) all: 0.245 / Net I/σ(I): 9 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5JMN Resolution: 2.8→49.15 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.898 / SU B: 19.088 / SU ML: 0.334 / SU R Cruickshank DPI: 0.6589 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.659 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.64 Å2 / Biso mean: 59.131 Å2 / Biso min: 12.77 Å2
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Refinement step | Cycle: final / Resolution: 2.8→49.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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