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Yorodumi- PDB-5b6y: A three dimensional movie of structural changes in bacteriorhodop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b6y | ||||||
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Title | A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 36.2 us after photoexcitation | ||||||
Components | Bacteriorhodopsin | ||||||
Keywords | PROTON TRANSPORT / bacteriorhodopsin / XFEL / time-resolved serial femtosecond crystallography / SACLA | ||||||
Function / homology | Function and homology information light-driven active monoatomic ion transmembrane transporter activity / 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: 2.1 Å | ||||||
Authors | Royant, A. / Nango, E. / Nakane, T. / Tanaka, T. / Arima, T. / Neutze, R. / Iwata, S. | ||||||
Citation | Journal: Science / Year: 2016 Title: A three-dimensional movie of structural changes in bacteriorhodopsin Authors: Nango, E. / Royant, A. / Kubo, M. / Nakane, T. / Wickstrand, C. / Kimura, T. / Tanaka, T. / Tono, K. / Song, C. / Tanaka, R. / Arima, T. / Yamashita, A. / Kobayashi, J. / Hosaka, T. / ...Authors: Nango, E. / Royant, A. / Kubo, M. / Nakane, T. / Wickstrand, C. / Kimura, T. / Tanaka, T. / Tono, K. / Song, C. / Tanaka, R. / Arima, T. / Yamashita, A. / Kobayashi, J. / Hosaka, T. / Mizohata, E. / Nogly, P. / Sugahara, M. / Nam, D. / Nomura, T. / Shimamura, T. / Im, D. / Fujiwara, T. / Yamanaka, Y. / Jeon, B. / Nishizawa, T. / Oda, K. / Fukuda, M. / Andersson, R. / Bath, P. / Dods, R. / Davidsson, J. / Matsuoka, S. / Kawatake, S. / Murata, M. / Nureki, O. / Owada, S. / Kameshima, T. / Hatsui, T. / Joti, Y. / Schertler, G. / Yabashi, M. / Bondar, A.N. / Standfuss, J. / Neutze, R. / Iwata, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b6y.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b6y.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 5b6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b6y_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5b6y_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5b6y_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 5b6y_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/5b6y ftp://data.pdbj.org/pub/pdb/validation_reports/b6/5b6y | HTTPS FTP |
-Related structure data
Related structure data | 5b6vSC 5b6wC 5b6xC 5b6zC 5h2hC 5h2iC 5h2jC 5h2kC 5h2lC 5h2mC 5h2nC 5h2oC 5h2pC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1337005 / Data set type: diffraction image 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: 26814.412 Da / Num. of mol.: 1 / Fragment: UNP residues 14-261 / Source method: isolated from a natural source Source: (natural) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halophile) Strain: ATCC 700922 / JCM 11081 / NRC-1 / References: UniProt: P02945 |
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-Non-polymers , 11 types, 37 molecules
#2: Chemical | ChemComp-RET / | ||||||||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-TRD / | #5: Chemical | ChemComp-D10 / | #6: Chemical | ChemComp-HP6 / | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-DD9 / | #11: Chemical | ChemComp-C14 / | #12: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | Ligands TRD, D10, HP6, OCT, MYS, UND, DD9, and C14 are modeled as a lipid fragment. |
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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: 2.35 Å3/Da / Density % sol: 47.77 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: 0.1M Na/K phosphate pH5.4, 30% PEG 2000 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.63 Å |
Detector | Type: MPCCD / Detector: CCD / Date: Feb 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.63 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→39.92 Å / Num. obs: 14513 / % possible obs: 100 % / Redundancy: 242 % / Net I/σ(I): 9.27 |
Reflection shell | Resolution: 2→2.07 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B6V Resolution: 2.1→21.912 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.05 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→21.912 Å
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Refine LS restraints |
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LS refinement shell |
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