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- PDB-7zn9: Crystal structure of the light-driven inward proton pump xenorhod... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zn9 | ||||||
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Title | Crystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the M state at pH 7.0 in the presence of sodium at 100K | ||||||
![]() | xenorhodopsin | ||||||
![]() | MEMBRANE PROTEIN / retinal / rhodopsin / xenorhodopsin / ion transport / isomerization / photocycle | ||||||
Function / homology | EICOSANE / OLEIC ACID / PHOSPHATE ION![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kovalev, K. / Tsybrov, F. / Alekseev, A. / Bourenkov, G. / Gordeliy, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanisms of inward transmembrane proton translocation. Authors: Kovalev, K. / Tsybrov, F. / Alekseev, A. / Shevchenko, V. / Soloviov, D. / Siletsky, S. / Bourenkov, G. / Agthe, M. / Nikolova, M. / von Stetten, D. / Astashkin, R. / Bukhdruker, S. / ...Authors: Kovalev, K. / Tsybrov, F. / Alekseev, A. / Shevchenko, V. / Soloviov, D. / Siletsky, S. / Bourenkov, G. / Agthe, M. / Nikolova, M. / von Stetten, D. / Astashkin, R. / Bukhdruker, S. / Chizhov, I. / Royant, A. / Kuzmin, A. / Gushchin, I. / Rosselli, R. / Rodriguez-Valera, F. / Ilyinskiy, N. / Rogachev, A. / Borshchevskiy, V. / Schneider, T.R. / 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 | ![]() | 170.8 KB | Display | ![]() |
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PDB format | ![]() | 134.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7zmyC ![]() 7zn0C ![]() 7zn3C ![]() 7zn8C ![]() 7znaC ![]() 7znbC ![]() 7zncC ![]() 7zndC ![]() 7zneC ![]() 7zngC ![]() 7znhC ![]() 7zniC ![]() 1xioS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: FME / Beg label comp-ID: FME / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 1 - 223 / Label seq-ID: 1 - 223
NCS ensembles :
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Components
#1: Protein | Mass: 25725.627 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-LFA / #3: Chemical | ChemComp-OLA / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.85 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.8 M Na/K-Pi pH 8.2 crystals soaked in 1.2 M Na/K-Pi pH 7.0 before harvesting |
-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: Mar 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.767 Å / Num. obs: 38234 / % possible obs: 96.3 % / Redundancy: 13.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.177 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.3→2.37 Å / Rmerge(I) obs: 2.464 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1912 / CC1/2: 0.569 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XIO Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.621 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.385 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.6 Å2 / Biso mean: 36.925 Å2 / Biso min: 17.21 Å2
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Refinement step | Cycle: final / Resolution: 2.3→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 / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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