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- PDB-7zmy: 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: 7zmy | ||||||
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Title | Crystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the ground state at pH 8.2 in the presence of sodium at 100K | ||||||
![]() | xenorhodopsin | ||||||
![]() | MEMBRANE PROTEIN / retinal / rhodopsin / xenorhodopsin / ion transport / isomerization / photocycle | ||||||
Function / homology | EICOSANE / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 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 | ![]() | 175.4 KB | Display | ![]() |
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PDB format | ![]() | 137.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 9.4 MB | Display | ![]() |
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Full document | ![]() | 9.4 MB | Display | |
Data in XML | ![]() | 35.6 KB | Display | |
Data in CIF | ![]() | 47.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zn0C ![]() 7zn3C ![]() 7zn8C ![]() 7zn9C ![]() 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 / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 25725.627 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 352 molecules ![](data/chem/img/LFA.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-LFA / #3: Chemical | ChemComp-OLA / #4: Chemical | ChemComp-OLC / ( | #5: Chemical | #6: Chemical | #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: 2.89 Å3/Da / Density % sol: 57.49 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: 0.8 M Na/K-Pi pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 20, 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: 1.7→49.799 Å / Num. obs: 91083 / % possible obs: 93.12 % / Redundancy: 13.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.7→1.742 Å / Rmerge(I) obs: 3.353 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4556 / CC1/2: 0.352 / % possible all: 78.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XIO Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.423 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.098 / 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: 123.18 Å2 / Biso mean: 33.56 Å2 / Biso min: 18.34 Å2
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Refinement step | Cycle: final / Resolution: 1.7→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: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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