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Yorodumi- PDB-7o8i: NmHR light state structure at 1 us after photoexcitation determin... -
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-Basic information
Entry | Database: PDB / ID: 7o8i | ||||||
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Title | NmHR light state structure at 1 us after photoexcitation determined by serial femtosecond crystallography (with extrapolated, dark and light dataset) | ||||||
Components | Chloride pumping rhodopsin | ||||||
Keywords | MEMBRANE PROTEIN / chloride pump / rhodopsin | ||||||
Function / homology | Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / plasma membrane / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Chloride pumping rhodopsin Function and homology information | ||||||
Biological species | Nonlabens marinus S1-08 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | 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 | Switzerland, 1items
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Citation | Journal: Science / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o8i.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o8i.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 7o8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o8i_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7o8i_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7o8i_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 7o8i_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/7o8i ftp://data.pdbj.org/pub/pdb/validation_reports/o8/7o8i | HTTPS FTP |
-Related structure data
Related structure data | 7o8fC 7o8gC 7o8hC 7o8jC 7o8kC 7o8lC 7o8mC 7o8nC 7o8oC 7o8pC 7o8qC 7o8rC 7o8sC 7o8tC 7o8uC 7o8vC 7o8yC 7o8zC 5b2nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Nonlabens marinus S1-08 (bacteria) / Gene: ClR, NMS_1267 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: W8VZW3 |
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-Non-polymers , 5 types, 78 molecules
#2: Chemical | ChemComp-RET / | ||||||
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#3: Chemical | #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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 MgCl2, 100 mM NaCl, 34% PEG400 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1 Å |
Detector | Type: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Sep 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→13.5 Å / Num. obs: 112288 / % possible obs: 100 % / Redundancy: 179 % / Biso Wilson estimate: 18.22 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.45→1.48 Å / Num. unique obs: 5433 / CC1/2: 0.24 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B2N Resolution: 1.8→13.45 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 36.18 / 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: 62.4 Å2 / Biso mean: 22.2601 Å2 / Biso min: 5.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→13.45 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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