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Open data
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Basic information
Entry | Database: PDB / ID: 5en5 | ||||||
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Title | Apo structure of bacterial efflux pump. | ||||||
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![]() | TRANSPORT PROTEIN / Efflux pump | ||||||
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 | ![]() ![]() Ribosome display vector pRDV (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sjuts, H. / Ornik, A.R. / Pos, K.M. | ||||||
![]() | ![]() Title: Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives. Authors: Sjuts, H. / Vargiu, A.V. / Kwasny, S.M. / Nguyen, S.T. / Kim, H.S. / Ding, X. / Ornik, A.R. / Ruggerone, P. / Bowlin, T.L. / Nikaido, H. / Pos, K.M. / Opperman, T.J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 431.1 KB | Display | ![]() |
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PDB format | ![]() | 350.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.5 KB | Display | ![]() |
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Full document | ![]() | 475.2 KB | Display | |
Data in XML | ![]() | 76.9 KB | Display | |
Data in CIF | ![]() | 108.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5enoC ![]() 5enpC ![]() 5enqC ![]() 5enrC ![]() 5ensC ![]() 5entC ![]() 4dx5S 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
#1: Protein | Mass: 65740.656 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: acrB, acrE, b0462, JW0451 / Production host: ![]() ![]() #2: Protein | Mass: 18317.566 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ribosome display vector pRDV (others) / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH6.5, 0.21 M NaCl, 11.5 % PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 122373 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.987 / Rmerge(I) obs: 0.191 / Net I/σ(I): 6.75 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.212 / CC1/2: 0.462 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DX5 Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.048 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.226 / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.278 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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