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- PDB-6tk6: Femtosecond to millisecond structural changes in a light-driven s... -
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Basic information
Entry | Database: PDB / ID: 6tk6 | ||||||||||||||||||||||||||||||
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Title | Femtosecond to millisecond structural changes in a light-driven sodium pump: Dark structure in neutral conditions with attached light datasets at 800fs, 2ps, 100ps, 1ns, 16ns, 1us, 30us, 150us, 1ms and 20ms | ||||||||||||||||||||||||||||||
![]() | Sodium pumping rhodopsin | ||||||||||||||||||||||||||||||
![]() | MEMBRANE PROTEIN / Sodium pumping rhodopsin / time-resolved / serial femtosecond crystallograpy / room-temperature | ||||||||||||||||||||||||||||||
Function / homology | ![]() | ||||||||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
![]() | Skopintsev, P. / Ehrenberg, D. / Weinert, T. / James, D. / Kar, R. / Johnson, P. / Ozerov, D. / Furrer, A. / Martiel, I. / Dworkowski, F. ...Skopintsev, P. / Ehrenberg, D. / Weinert, T. / James, D. / Kar, R. / Johnson, P. / Ozerov, D. / Furrer, A. / Martiel, I. / Dworkowski, F. / Nass, K. / Knopp, G. / Cirelli, C. / Gashi, D. / Mous, S. / Wranik, M. / Gruhl, T. / Kekilli, D. / Bruenle, S. / Deupi, X. / Schertler, G.F.X. / Benoit, R. / Panneels, V. / Nogly, P. / Schapiro, I. / Milne, C. / Heberle, J. / Standfuss, J. | ||||||||||||||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Femtosecond-to-millisecond structural changes in a light-driven sodium pump. Authors: Skopintsev, P. / Ehrenberg, D. / Weinert, T. / James, D. / Kar, R.K. / Johnson, P.J.M. / Ozerov, D. / Furrer, A. / Martiel, I. / Dworkowski, F. / Nass, K. / Knopp, G. / Cirelli, C. / Arrell, ...Authors: Skopintsev, P. / Ehrenberg, D. / Weinert, T. / James, D. / Kar, R.K. / Johnson, P.J.M. / Ozerov, D. / Furrer, A. / Martiel, I. / Dworkowski, F. / Nass, K. / Knopp, G. / Cirelli, C. / Arrell, C. / Gashi, D. / Mous, S. / Wranik, M. / Gruhl, T. / Kekilli, D. / Brunle, S. / Deupi, X. / Schertler, G.F.X. / Benoit, R.M. / Panneels, V. / Nogly, P. / Schapiro, I. / Milne, C. / Heberle, J. / Standfuss, J. | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.4 KB | Display | ![]() |
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PDB format | ![]() | 56.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tk1C ![]() 6tk2C ![]() 6tk3C ![]() 6tk4C ![]() 6tk5C ![]() 6tk7C ![]() 3x3cS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 32894.859 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: Chemical | ChemComp-LFA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.84 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 4.4 Details: 200 mM Sodium Acetate pH 4.4, 150 mM MgCl2, 35% PEG 200 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Feb 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→12.43 Å / Num. obs: 31741 / % possible obs: 77.2 % / Redundancy: 1328 % / CC1/2: 1 / R split: 0.049 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.6→2.3 Å / Redundancy: 872 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 12867 / CC1/2: 0.95 / R split: 0.3 / % possible all: 35.4 |
Serial crystallography measurement | Focal spot size: 3.5 µm2 / Pulse photon energy: 12.4 keV / XFEL pulse repetition rate: 50 Hz |
Serial crystallography sample delivery | Description: High viscosity injector / Method: injection |
Serial crystallography sample delivery injection | Injector nozzle: capillary / Jet diameter: 75 µm |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3x3c Resolution: 1.6→12.426 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.53 / 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: 108.72 Å2 / Biso mean: 39.2853 Å2 / Biso min: 16.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→12.426 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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