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- PDB-7q37: Crystal structure of proton pump MAR rhodopsin pressurized with k... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7q37 | ||||||
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Title | Crystal structure of proton pump MAR rhodopsin pressurized with krypton | ||||||
![]() | Bacteriorhodopsin | ||||||
![]() | MEMBRANE PROTEIN / proton pump rhodopsin | ||||||
Function / homology | Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / HEXANE / KRYPTON / EICOSANE / RETINAL / Bacteriorhodopsin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Melnikov, I. / Rulev, M. / Astashkin, R. / Kovalev, K. / Carpentier, P. / Gordeliy, V. / Popov, A. | ||||||
Funding support | 1items
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![]() | ![]() Title: High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action. Authors: Melnikov, I. / Orekhov, P. / Rulev, M. / Kovalev, K. / Astashkin, R. / Bratanov, D. / Ryzhykau, Y. / Balandin, T. / Bukhdruker, S. / Okhrimenko, I. / Borshchevskiy, V. / Bourenkov, G. / ...Authors: Melnikov, I. / Orekhov, P. / Rulev, M. / Kovalev, K. / Astashkin, R. / Bratanov, D. / Ryzhykau, Y. / Balandin, T. / Bukhdruker, S. / Okhrimenko, I. / Borshchevskiy, V. / Bourenkov, G. / Mueller-Dieckmann, C. / van der Linden, P. / Carpentier, P. / Leonard, G. / Gordeliy, V. / Popov, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.9 KB | Display | ![]() |
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PDB format | ![]() | 46.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.2 MB | Display | ![]() |
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Full document | ![]() | 5.2 MB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q35C ![]() 7q36C ![]() 7q38C ![]() 5jsiS 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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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24305.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 5 types, 138 molecules ![](data/chem/img/RET.gif)
![](data/chem/img/LFA.gif)
![](data/chem/img/HEX.gif)
![](data/chem/img/KR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LFA.gif)
![](data/chem/img/HEX.gif)
![](data/chem/img/KR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-RET / | ||||||
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#3: Chemical | ChemComp-LFA / #4: Chemical | ChemComp-HEX / #5: Chemical | ChemComp-KR / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.05 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 2.6 M ammonium sulfate, 0.1 M sodium acetate, pH 5.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.861 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→100 Å / Num. obs: 22357 / % possible obs: 99.4 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rrim(I) all: 0.14 / Net I/σ(I): 7.74 |
Reflection shell | Resolution: 2.25→2.35 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.14 / Num. unique obs: 2971 / CC1/2: 0.491 / Rrim(I) all: 1.299 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JSI Resolution: 2.25→59.43 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.704 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 34.645 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→59.43 Å
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Refine LS restraints |
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