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- PDB-7o8z: Anomalous bromide substructure of NmHR under continuous illuminat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o8z | ||||||
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Title | Anomalous bromide substructure of NmHR under continuous illumination determined at 13.7 keV with serial crystallography | ||||||
![]() | Chloride pumping rhodopsin | ||||||
![]() | MEMBRANE PROTEIN / chloride pump / rhodopsin | ||||||
Function / homology | Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / plasma membrane / BROMIDE ION / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Chloride pumping rhodopsin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Mous, S. / Gotthard, G. / Ehrenberg, D. / Sen, S. / James, D. / Johnson, P. / Weinert, T. / Nass, K. / Furrer, A. / Kekilli, D. ...Mous, S. / Gotthard, G. / Ehrenberg, D. / Sen, S. / James, D. / Johnson, P. / Weinert, T. / Nass, K. / Furrer, A. / Kekilli, D. / Ma, P. / Bruenle, S. / Casadei, C. / Martiel, I. / Dworkowski, F. / Gashi, D. / Skopintsev, P. / Wranik, M. / Knopp, G. / Panepucci, E. / Panneels, V. / Cirelli, C. / Ozerov, D. / Schertler, G. / Wang, M. / Milne, C. / Standfuss, J. / Schapiro, I. / Heberle, J. / Nogly, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Dynamics and mechanism of a light-driven chloride pump. Authors: Mous, S. / Gotthard, G. / Ehrenberg, D. / Sen, S. / Weinert, T. / Johnson, P.J.M. / James, D. / Nass, K. / Furrer, A. / Kekilli, D. / Ma, P. / Brunle, S. / Casadei, C.M. / Martiel, I. / ...Authors: Mous, S. / Gotthard, G. / Ehrenberg, D. / Sen, S. / Weinert, T. / Johnson, P.J.M. / James, D. / Nass, K. / Furrer, A. / Kekilli, D. / Ma, P. / Brunle, S. / Casadei, C.M. / Martiel, I. / Dworkowski, F. / Gashi, D. / Skopintsev, P. / Wranik, M. / Knopp, G. / Panepucci, E. / Panneels, V. / Cirelli, C. / Ozerov, D. / Schertler, G.F.X. / Wang, M. / Milne, C. / Standfuss, J. / Schapiro, I. / Heberle, J. / Nogly, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75 KB | Display | ![]() |
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PDB format | ![]() | 52.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o8fC ![]() 7o8gC ![]() 7o8hC ![]() 7o8iC ![]() 7o8jC ![]() 7o8kC ![]() 7o8lC ![]() 7o8mC ![]() 7o8nC ![]() 7o8oC ![]() 7o8pC ![]() 7o8qC ![]() 7o8rC ![]() 7o8sC ![]() 7o8tC ![]() 7o8uC ![]() 7o8vC ![]() 7o8yC ![]() 5b2nS 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32913.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 66 molecules ![](data/chem/img/RET.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-RET / | ||||||
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#3: Chemical | ChemComp-BR / #4: Chemical | #5: Chemical | ChemComp-OLA / #6: 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: 2.37 Å3/Da / Density % sol: 48.15 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 4.5 Details: 50 mM sodium acetate (pH 4.5), 150 mM MgBr2, 100 mM NaBr, 34% PEG400 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.905 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→58.41 Å / Num. obs: 56138 / % possible obs: 100 % / Redundancy: 664 % / Biso Wilson estimate: 27.83 Å2 / CC1/2: 0.42 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Num. unique obs: 5625 / CC1/2: 0.42 |
Serial crystallography sample delivery | Method: injection |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5B2N Resolution: 1.8→52.24 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.78 / 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: 136.39 Å2 / Biso mean: 50.6535 Å2 / Biso min: 33.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→52.24 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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