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- PDB-6yby: Crystal structure of the D116N mutant of the light-driven sodium ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yby | ||||||||||||||||||
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Title | Crystal structure of the D116N mutant of the light-driven sodium pump KR2 in the monomeric form, pH 4.6 | ||||||||||||||||||
![]() | Sodium pumping rhodopsin | ||||||||||||||||||
![]() | MEMBRANE PROTEIN / rhodopsin / ion pumping / retinal / sodium pump / intermediate state | ||||||||||||||||||
Function / homology | Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / EICOSANE / RETINAL / Sodium pumping rhodopsin![]() | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Kovalev, K. / Gushchin, I. / Gordeliy, V. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Molecular mechanism of light-driven sodium pumping. Authors: Kovalev, K. / Astashkin, R. / Gushchin, I. / Orekhov, P. / Volkov, D. / Zinovev, E. / Marin, E. / Rulev, M. / Alekseev, A. / Royant, A. / Carpentier, P. / Vaganova, S. / Zabelskii, D. / ...Authors: Kovalev, K. / Astashkin, R. / Gushchin, I. / Orekhov, P. / Volkov, D. / Zinovev, E. / Marin, E. / Rulev, M. / Alekseev, A. / Royant, A. / Carpentier, P. / Vaganova, S. / Zabelskii, D. / Baeken, C. / Sergeev, I. / Balandin, T. / Bourenkov, G. / Carpena, X. / Boer, R. / Maliar, N. / Borshchevskiy, 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 | ![]() | 86.9 KB | Display | ![]() |
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PDB format | ![]() | 62.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.5 MB | Display | ![]() |
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Full document | ![]() | 5.7 MB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xytC ![]() 6ybzC ![]() 6yc0C ![]() 6yc1C ![]() 6yc2C ![]() 6yc3C ![]() 6yc4C ![]() 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 30907.756 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-NA / | ||||||
#3: Chemical | ChemComp-LFA / #4: Chemical | ChemComp-RET / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.95 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 4.6 / Details: 2 M NaMal pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 26, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→40.81 Å / Num. obs: 37771 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Net I/σ(I): 16.2 / Num. measured all: 249134 / Scaling rejects: 12 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4xtl Resolution: 1.8→19.83 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.571 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.111 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: 170.56 Å2 / Biso mean: 43.739 Å2 / Biso min: 21.65 Å2
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Refinement step | Cycle: final / Resolution: 1.8→19.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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