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- PDB-8h79: The crystal structure of cyanorhodopsin-II (CyR-II) P7104R from N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h79 | |||||||||
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Title | The crystal structure of cyanorhodopsin-II (CyR-II) P7104R from Nodosilinea nodulosa PCC 7104 | |||||||||
![]() | cyanorhodopsin-II (CyR-II) P7104R | |||||||||
![]() | MEMBRANE PROTEIN / RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin Cyanobacteria | |||||||||
Function / homology | TETRADECANE / HEXANE / N-OCTANE / HEXADECANE / RETINAL![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hosaka, T. / Kimura-Someya, T. / Shirouzu, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cyanorhodopsin-II: diverse proton-pumping rhodopsins in the cyanobacterial lineage illuminated by large-scale metagenomic Authors: Hasegawa, M. / Hosaka, T. / Kojima, K. / Nishimura, Y. / Kurihara, M. / Nakajima, Y. / Ishizuka-Katsura, Y. / Kimura-Someya, T. / Shirouzu, M. / Sudo, Y. / Yoshizawa, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.2 KB | Display | ![]() |
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PDB format | ![]() | 46 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 689.1 KB | Display | ![]() |
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Full document | ![]() | 690.7 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 15.3 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 | 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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Details | There is no clear evidence that the assembly should be a monomer or trimer. |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28417.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Sequence has been deposited to Genbank with accession number WP_017301364.1 Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 9 types, 59 molecules ![](data/chem/img/RET.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HEX.gif)
![](data/chem/img/OCT.gif)
![](data/chem/img/C14.gif)
![](data/chem/img/R16.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HEX.gif)
![](data/chem/img/OCT.gif)
![](data/chem/img/C14.gif)
![](data/chem/img/R16.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-RET / | ||||||||||||
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#3: Chemical | ChemComp-PG4 / | ||||||||||||
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-R16 / | #8: Chemical | ChemComp-SO4 / | #9: Chemical | ChemComp-CL / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.43 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.8 / Details: 100mM HEPES, 46% PEG 400, 400mM lithium sulfate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.07→49.6 Å / Num. obs: 17190 / % possible obs: 99.8 % / Redundancy: 12.407 % / Biso Wilson estimate: 27.86 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.227 / Rrim(I) all: 0.236 / Χ2: 0.97 / Net I/σ(I): 10.25 / Num. measured all: 213269 / Scaling rejects: 495 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1C3W Resolution: 2.07→49.6 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.66 / 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: 78.47 Å2 / Biso mean: 29.5547 Å2 / Biso min: 13.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.07→49.6 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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