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Yorodumi- PDB-6g7l: Retinal isomerization in bacteriorhodopsin revealed by a femtosec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g7l | |||||||||||||||
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Title | Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: 8.3 ms state structure | |||||||||||||||
Components | Bacteriorhodopsin | |||||||||||||||
Keywords | PROTON TRANSPORT / retinal isomerization / ultrafast / femtosecond / room temperature / time resolved crystallography | |||||||||||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Halobacterium salinarum (Halophile) | |||||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||||||||
Authors | Nogly, P. / Weinert, T. / James, D. / Cabajo, S. / Ozerov, D. / Furrer, A. / Gashi, D. / Borin, V. / Skopintsev, P. / Jaeger, K. ...Nogly, P. / Weinert, T. / James, D. / Cabajo, S. / Ozerov, D. / Furrer, A. / Gashi, D. / Borin, V. / Skopintsev, P. / Jaeger, K. / Nass, K. / Bath, P. / Bosman, R. / Koglin, J. / Seaberg, M. / Lane, T. / Kekilli, D. / Bruenle, S. / Tanaka, T. / Wu, W. / Milne, C. / White, T. / Barty, A. / Weierstall, U. / Panneels, V. / Nango, E. / Iwata, S. / Hunter, M. / Schapiro, I. / Schertler, G. / Neutze, R. / Standfuss, J. | |||||||||||||||
Funding support | Switzerland, 4items
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Citation | Journal: Science / Year: 2018 Title: Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Authors: Nogly, P. / Weinert, T. / James, D. / Carbajo, S. / Ozerov, D. / Furrer, A. / Gashi, D. / Borin, V. / Skopintsev, P. / Jaeger, K. / Nass, K. / Bath, P. / Bosman, R. / Koglin, J. / Seaberg, M. ...Authors: Nogly, P. / Weinert, T. / James, D. / Carbajo, S. / Ozerov, D. / Furrer, A. / Gashi, D. / Borin, V. / Skopintsev, P. / Jaeger, K. / Nass, K. / Bath, P. / Bosman, R. / Koglin, J. / Seaberg, M. / Lane, T. / Kekilli, D. / Brunle, S. / Tanaka, T. / Wu, W. / Milne, C. / White, T. / Barty, A. / Weierstall, U. / Panneels, V. / Nango, E. / Iwata, S. / Hunter, M. / Schapiro, I. / Schertler, G. / Neutze, R. / Standfuss, J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g7l.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g7l.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 6g7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/6g7l ftp://data.pdbj.org/pub/pdb/validation_reports/g7/6g7l | HTTPS FTP |
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-Related structure data
Related structure data | 6g7hC 6g7iC 6g7jC 6g7kC 5j7aS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28270.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halophile) References: UniProt: P02945 | ||||
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#2: Chemical | ChemComp-RET / | ||||
#3: Chemical | ChemComp-LI1 / #4: Chemical | ChemComp-OLC / ( #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.17 % / Description: plates |
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Crystal grow | Temperature: 294 K / Method: lipidic cubic phase / pH: 5.6 / Details: 100 mM Na/K Phosphate buffer pH 5.6 30 % PEG 2000 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Jun 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→18.517 Å / Num. obs: 18134 / % possible obs: 94.2 % / Redundancy: 2046.2 % / Net I/σ(I): 19.62 |
Reflection shell | Resolution: 1.9→1.99 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J7A Resolution: 1.9→18.517 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→18.517 Å
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Refine LS restraints |
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LS refinement shell |
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