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- PDB-6yc3: 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: 6yc3 | ||||||||||||||||||
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Title | Crystal structure of the light-driven sodium pump KR2 in the pentameric form, pH 8.0 | ||||||||||||||||||
![]() | 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 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 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 | ![]() | 328.1 KB | Display | ![]() |
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PDB format | ![]() | 267.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 16.3 MB | Display | ![]() |
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Full document | ![]() | 16.4 MB | Display | |
Data in XML | ![]() | 71.9 KB | Display | |
Data in CIF | ![]() | 92.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xytC ![]() 6ybyC ![]() 6ybzC ![]() 6yc0C ![]() 6yc1C ![]() 6yc2C ![]() 6yc4C ![]() 6rew 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: 1 - 273
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: 30807.639 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Sugar | ChemComp-BOG / |
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-Non-polymers , 5 types, 698 molecules ![](data/chem/img/OLC.gif)
![](data/chem/img/LFA.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LFA.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-OLC / ( #3: Chemical | ChemComp-LFA / #5: Chemical | ChemComp-RET / #6: Chemical | ChemComp-NA / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.7 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8 / Details: 1.2 M NaMal 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 16M / Detector: PIXEL / Date: Oct 5, 2019 | ||||||||||||||||||||||||||||||
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→48.16 Å / Num. obs: 144508 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.03 / Rrim(I) all: 0.082 / Net I/σ(I): 13.2 / Num. measured all: 1101707 / Scaling rejects: 6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6rew ![]() 6rew Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.522 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.122 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: 223.33 Å2 / Biso mean: 47.553 Å2 / Biso min: 23.5 Å2
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Refinement step | Cycle: final / Resolution: 2→20 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→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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