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- PDB-7bmh: Crystal structure of a light-driven proton pump LR (Mac) from Lep... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bmh | |||||||||||||||
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Title | Crystal structure of a light-driven proton pump LR (Mac) from Leptosphaeria maculans | |||||||||||||||
![]() | Opsin | |||||||||||||||
![]() | MEMBRANE PROTEIN / rhodopsin / bacteriorhodopsin / retinal / optogenetics / proton pump / photocycle / eukaryotic rhodopsin / ion transport | |||||||||||||||
Function / homology | ![]() : / photoreceptor activity / phototransduction / monoatomic ion channel activity / membrane => GO:0016020 Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Kovalev, K. / Zabelskii, D. / Dmitrieva, N. / Volkov, O. / Shevchenko, V. / Astashkin, R. / Zinovev, E. / Gordeliy, V. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure-based insights into evolution of rhodopsins. Authors: Zabelskii, D. / Dmitrieva, N. / Volkov, O. / Shevchenko, V. / Kovalev, K. / Balandin, T. / Soloviov, D. / Astashkin, R. / Zinovev, E. / Alekseev, A. / Round, E. / Polovinkin, V. / Chizhov, I. ...Authors: Zabelskii, D. / Dmitrieva, N. / Volkov, O. / Shevchenko, V. / Kovalev, K. / Balandin, T. / Soloviov, D. / Astashkin, R. / Zinovev, E. / Alekseev, A. / Round, E. / Polovinkin, V. / Chizhov, I. / Rogachev, A. / Okhrimenko, I. / Borshchevskiy, V. / Chupin, V. / Buldt, G. / Yutin, N. / Bamberg, E. / Koonin, 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 | ![]() | 125.6 KB | Display | ![]() |
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PDB format | ![]() | 92.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 943.7 KB | Display | ![]() |
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Full document | ![]() | 886 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 31.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1c3wS S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35970.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ops / Production host: ![]() #2: Chemical | ChemComp-LFA / #3: Chemical | ChemComp-OLA / #4: 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: 2.31 Å3/Da / Density % sol: 46.83 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100 mM HEPES pH 7.0, 4% PEG 3350, 1 M sodium malonate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 28, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→49.39 Å / Num. obs: 34762 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 31.58 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.086 / Rrim(I) all: 0.193 / Net I/σ(I): 5.7 / Num. measured all: 168155 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1C3W Resolution: 2.2→19.92 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.05 Å2 / Biso mean: 36.1578 Å2 / Biso min: 17.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→19.92 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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