[English] 日本語
![](img/lk-miru.gif)
- PDB-7aky: Crystal structure of the viral rhodopsin OLPVR1 in P21212 space group -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7aky | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the viral rhodopsin OLPVR1 in P21212 space group | ||||||||||||
![]() | viral rhodopsin OLPVR1 | ||||||||||||
![]() | MEMBRANE PROTEIN / rhodopsin / viral rhodopsin / giant virus / ion channel / retinal / ion transport / light-gated channel / channelrhodopsin / bacteriorhodopsin | ||||||||||||
Function / homology | ![]() photoreceptor activity / phototransduction / monoatomic ion channel activity / membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kovalev, K. / Zabelskii, D. / Alekseev, A. / Astashkin, R. / Gordeliy, V. | ||||||||||||
Funding support | ![]() ![]()
| ||||||||||||
![]() | ![]() Title: Viral rhodopsins 1 are an unique family of light-gated cation channels. Authors: Zabelskii, D. / Alekseev, A. / Kovalev, K. / Rankovic, V. / Balandin, T. / Soloviov, D. / Bratanov, D. / Savelyeva, E. / Podolyak, E. / Volkov, D. / Vaganova, S. / Astashkin, R. / Chizhov, I. ...Authors: Zabelskii, D. / Alekseev, A. / Kovalev, K. / Rankovic, V. / Balandin, T. / Soloviov, D. / Bratanov, D. / Savelyeva, E. / Podolyak, E. / Volkov, D. / Vaganova, S. / Astashkin, R. / Chizhov, I. / Yutin, N. / Rulev, M. / Popov, A. / Eria-Oliveira, A.S. / Rokitskaya, T. / Mager, T. / Antonenko, Y. / Rosselli, R. / Armeev, G. / Shaitan, K. / Vivaudou, M. / Buldt, G. / Rogachev, A. / Rodriguez-Valera, F. / Kirpichnikov, M. / Moser, T. / Offenhausser, A. / Willbold, D. / Koonin, E. / Bamberg, E. / Gordeliy, V. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 133.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 102.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7akwC ![]() 7akxC ![]() 6sqgS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 28366.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: 162281038 / Production host: ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-LFA / #3: Chemical | ChemComp-97N / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.46 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8.2 Details: 10 mM CaCl2, 10 mM MgCl2, 24% PEG 6000, 100mM Tris (pH 8.2), monopalmitolein |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 6, 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: 1.4→48.59 Å / Num. obs: 57845 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Rrim(I) all: 0.078 / Net I/σ(I): 12.3 / Num. measured all: 364526 / Scaling rejects: 11 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6sqg Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.546 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 122.03 Å2 / Biso mean: 24.189 Å2 / Biso min: 12.09 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|