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- PDB-6rfa: Crystal structure of the H30K mutant of the light-driven sodium p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rfa | ||||||||||||||||||
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Title | Crystal structure of the H30K mutant of the light-driven sodium pump KR2 in the monomeric form, pH 8.0 | ||||||||||||||||||
![]() | Sodium pumping rhodopsin | ||||||||||||||||||
![]() | MEMBRANE PROTEIN / light-driven sodium pump / ion translocation / retinal / rhodopsin | ||||||||||||||||||
Function / homology | ![]() | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Kovalev, K. / Polovinkin, V. / Gushchin, I. / Borshchevskiy, V. / Gordeliy, V. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure and mechanisms of sodium-pumping KR2 rhodopsin. Authors: Kovalev, K. / Polovinkin, V. / Gushchin, I. / Alekseev, A. / Shevchenko, V. / Borshchevskiy, V. / Astashkin, R. / Balandin, T. / Bratanov, D. / Vaganova, S. / Popov, A. / Chupin, V. / Buldt, ...Authors: Kovalev, K. / Polovinkin, V. / Gushchin, I. / Alekseev, A. / Shevchenko, V. / Borshchevskiy, V. / Astashkin, R. / Balandin, T. / Bratanov, D. / Vaganova, S. / Popov, A. / Chupin, V. / 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 | ![]() | 81.1 KB | Display | ![]() |
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PDB format | ![]() | 57.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5 MB | Display | ![]() |
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Full document | ![]() | 4.9 MB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rexC ![]() 6rezC ![]() 6rf0C ![]() 6rf1C ![]() 6rf3C ![]() 6rf4C ![]() 6rf5C ![]() 6rf6C ![]() 6rf7C ![]() 6rf9C ![]() 6rfbC ![]() 6rfcC ![]() 4xtlS 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32602.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 75 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/LFA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LFA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | ChemComp-LFA / #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-RET / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.62 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: 2.0 M Sodium Malonate, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→42.09 Å / Num. obs: 21097 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.997 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.2→2.27 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1825 / CC1/2: 0.476 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XTL Resolution: 2.2→19.89 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.603 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.186 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 272.91 Å2 / Biso mean: 39.81 Å2 / Biso min: 19.01 Å2
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Refinement step | Cycle: final / Resolution: 2.2→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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