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- PDB-5jrf: Crystal structure of the light-driven sodium pump KR2 bound with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jrf | ||||||
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Title | Crystal structure of the light-driven sodium pump KR2 bound with iodide ions | ||||||
![]() | Sodium pumping rhodopsin | ||||||
![]() | TRANSPORT PROTEIN / membrane protein / sodium pump / iodide | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Melnikov, I. / Polovinkin, V. / Kovalev, K. / Shevchenko, V. / Gushchin, I. / Popov, A. / Gordeliy, V. | ||||||
![]() | ![]() Title: Fast iodide-SAD phasing for high-throughput membrane protein structure determination. Authors: Melnikov, I. / Polovinkin, V. / Kovalev, K. / Gushchin, I. / Shevtsov, M. / Shevchenko, V. / Mishin, A. / Alekseev, A. / Rodriguez-Valera, F. / Borshchevskiy, V. / Cherezov, V. / Leonard, G. ...Authors: Melnikov, I. / Polovinkin, V. / Kovalev, K. / Gushchin, I. / Shevtsov, M. / Shevchenko, V. / Mishin, A. / Alekseev, A. / Rodriguez-Valera, F. / Borshchevskiy, V. / Cherezov, V. / Leonard, G.A. / Gordeliy, V. / Popov, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.4 KB | Display | ![]() |
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PDB format | ![]() | 52.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 on special symmetry positions |
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Components
#1: Protein | Mass: 32879.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-LFA / #3: Chemical | ChemComp-IOD / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.86 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: in meso lipidic cubic phase crystallization |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.85 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→60 Å / Num. obs: 26628 / % possible obs: 99.2 % / Redundancy: 6.73 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Net I/σ(I): 10.25 |
Reflection shell | Resolution: 2.35→2.5 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 1.54 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 38.61 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→117.05 Å
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Refine LS restraints |
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