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- PDB-4xtn: Crystal structure of the light-driven sodium pump KR2 in the pent... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xtn | ||||||
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Title | Crystal structure of the light-driven sodium pump KR2 in the pentameric red form, pH 4.9 | ||||||
![]() | Sodium pumping rhodopsin | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gushchin, I. / Shevchenko, V. / Polovinkin, V. / Gordeliy, V. | ||||||
![]() | ![]() Title: Crystal structure of a light-driven sodium pump. Authors: Gushchin, I. / Shevchenko, V. / Polovinkin, V. / Kovalev, K. / Alekseev, A. / Round, E. / Borshchevskiy, V. / Balandin, T. / Popov, A. / Gensch, T. / Fahlke, C. / Bamann, C. / Willbold, D. / ...Authors: Gushchin, I. / Shevchenko, V. / Polovinkin, V. / Kovalev, K. / Alekseev, A. / Round, E. / Borshchevskiy, V. / Balandin, T. / Popov, A. / Gensch, T. / Fahlke, C. / Bamann, C. / Willbold, D. / Buldt, G. / Bamberg, E. / Gordeliy, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 582.3 KB | Display | ![]() |
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PDB format | ![]() | 479.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4xtlSC ![]() 4xtoC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32879.008 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-LFA / ![]() #4: Chemical | ChemComp-MPG / [( #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.57 % |
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Crystal grow![]() | Temperature: 293 K / Method: lipidic cubic phase Details: The crystals were grown using in meso crystallization technique |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→48.9 Å / Num. obs: 192342 / % possible obs: 96.2 % / Redundancy: 2.8 % / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.975 / Mean I/σ(I) obs: 1.2 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4XTL Resolution: 2.2→48.9 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.692 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.186 / 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: 35.945 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→48.9 Å
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Refine LS restraints |
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