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- PDB-6rf1: 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: 6rf1 | ||||||||||||||||||
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Title | Crystal structure of the light-driven sodium pump KR2 in the pentameric "wet" form | ||||||||||||||||||
![]() | 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 | ![]() | 308 KB | Display | ![]() |
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PDB format | ![]() | 251.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 8.4 MB | Display | ![]() |
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Full document | ![]() | 8.4 MB | Display | |
Data in XML | ![]() | 62.3 KB | Display | |
Data in CIF | ![]() | 78.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rexC ![]() 6rezC ![]() 6rf0C ![]() 6rf3C ![]() 6rf4C ![]() 6rf5C ![]() 6rf6C ![]() 6rf7C ![]() 6rf9C ![]() 6rfaC ![]() 6rfbC ![]() 6rfcC ![]() 4xtnS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 275 / Label seq-ID: 3 - 275
NCS ensembles :
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Components
-Protein / Sugars , 2 types, 10 molecules ABCDE![](data/chem/img/BOG.gif)
![](data/chem/img/BOG.gif)
#1: Protein | Mass: 32611.580 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Sugar | ChemComp-BOG / |
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-Non-polymers , 5 types, 267 molecules ![](data/chem/img/OLC.gif)
![](data/chem/img/LFA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LFA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-OLC / ( #3: Chemical | ChemComp-LFA / #4: Chemical | ChemComp-NA / #6: Chemical | ChemComp-RET / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.11 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: 3.4 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 EIGER X 4M / Detector: PIXEL / Date: Oct 3, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→48.13 Å / Num. obs: 52539 / % possible obs: 99.6 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.072 / Rrim(I) all: 0.16 / Net I/σ(I): 5.6 / Num. measured all: 236235 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4XTN chain D Resolution: 2.8→48.17 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.939 / SU B: 18.804 / SU ML: 0.316 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.463 / ESU R Free: 0.313 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: 197.1 Å2 / Biso mean: 61.866 Å2 / Biso min: 33.64 Å2
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Refinement step | Cycle: final / Resolution: 2.8→48.17 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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