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- PDB-7crj: Dark State Structure of Chloride ion pumping rhodopsin (ClR) with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7crj | ||||||||||||
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Title | Dark State Structure of Chloride ion pumping rhodopsin (ClR) with NTQ motif | ||||||||||||
![]() | Chloride pumping rhodopsin | ||||||||||||
![]() | MEMBRANE PROTEIN / chloride ion pumping rhodopsin / SFX / XFEL / ClR / NTQ | ||||||||||||
Function / homology | Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / plasma membrane / OLEIC ACID / RETINAL / Chloride pumping rhodopsin![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Yun, J.H. / Liu, H. / Lee, W.T. / Schmidt, M. | ||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Early-stage dynamics of chloride ion-pumping rhodopsin revealed by a femtosecond X-ray laser. Authors: Yun, J.H. / Li, X. / Yue, J. / Park, J.H. / Jin, Z. / Li, C. / Hu, H. / Shi, Y. / Pandey, S. / Carbajo, S. / Boutet, S. / Hunter, M.S. / Liang, M. / Sierra, R.G. / Lane, T.J. / Zhou, L. / ...Authors: Yun, J.H. / Li, X. / Yue, J. / Park, J.H. / Jin, Z. / Li, C. / Hu, H. / Shi, Y. / Pandey, S. / Carbajo, S. / Boutet, S. / Hunter, M.S. / Liang, M. / Sierra, R.G. / Lane, T.J. / Zhou, L. / Weierstall, U. / Zatsepin, N.A. / Ohki, M. / Tame, J.R.H. / Park, S.Y. / Spence, J.C.H. / Zhang, W. / Schmidt, M. / Lee, W. / Liu, H. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.3 KB | Display | ![]() |
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PDB format | ![]() | 51.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7criC ![]() 7crkC ![]() 7crlC ![]() 7crsC ![]() 7crtC ![]() 7crxC ![]() 7cryC ![]() 5g28S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29398.521 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-RET / | #4: Chemical | ChemComp-OLA / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.85 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 7 / Details: monoolein (1-oleoyl-rac-glycerol) |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Oct 21, 2018 / Frequency: 120 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20.9 Å / Num. obs: 40394 / % possible obs: 91.45 % / Redundancy: 424.2 % / Biso Wilson estimate: 12.13 Å2 / CC1/2: 0.9838 / CC star: 0.9959 / Net I/σ(I): 5.52 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 77 % / Num. unique obs: 4010 / CC1/2: 0.6769 / CC star: 0.8985 / % possible all: 74.84 |
Serial crystallography measurement | Collection time total: 6 hours / Focal spot size: 1 µm2 / Pulse duration: 100 fsec. / Pulse photon energy: 9.54 keV / Source distance: 0.09 m / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Description: LCP injector / Method: injection |
Serial crystallography sample delivery injection | Description: LCP injector / Injector diameter: 75 µm / Injector temperature: 293 K |
Serial crystallography data reduction | Crystal hits: 60000 / Frames indexed: 37044 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5G28 Resolution: 1.65→20.64 Å / SU ML: 0.1718 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.5557 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 17.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→20.64 Å
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Refine LS restraints |
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LS refinement shell |
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