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- PDB-8qqo: Continuously illuminated structure of Sensory Rhodopsin II solved... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qqo | |||||||||
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Title | Continuously illuminated structure of Sensory Rhodopsin II solved by serial millisecond crystallography | |||||||||
![]() | Sensory rhodopsin-2 | |||||||||
![]() | SIGNALING PROTEIN / SRII / serial millisecond crystallography / sensory rhodopsin / sensory rhodopsin II / SMX / SSX | |||||||||
Function / homology | ![]() photoreceptor activity / phototransduction / monoatomic ion channel activity / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bosman, R. / Ortolani, G. / Branden, G. / Neutze, R. | |||||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Structural basis of the prolonged photocycle of Sensory Rhodopsin II revealed by serial millisecond crystallography Authors: Bosman, R. / Ortolani, G. / Branden, G. / Neutze, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.5 KB | Display | ![]() |
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PDB format | ![]() | 72.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 892 KB | Display | ![]() |
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Full document | ![]() | 898.6 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pncC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26666.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-RET / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.47 % |
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Crystal grow | Temperature: 296 K / Method: lipidic cubic phase Details: CaCl2 150mM, Glycine 100mM, 38%(v/v) PEG 400, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 296 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0000342 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→44.9 Å / Num. obs: 16876 / % possible obs: 100 % / Redundancy: 256.1 % / Biso Wilson estimate: 30.74 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.47→2.5 Å / Num. unique obs: 16876 / CC1/2: 0.448 |
Serial crystallography sample delivery | Method: injection |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.47 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.47→44.88 Å
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Refine LS restraints |
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LS refinement shell |
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