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- PDB-5b6x: A three dimensional movie of structural changes in bacteriorhodop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b6x | ||||||
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Title | A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 760 ns after photoexcitation | ||||||
![]() | Bacteriorhodopsin | ||||||
![]() | PROTON TRANSPORT / bacteriorhodopsin / XFEL / time- resolved serial femtosecond crystallography / SACLA | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Royant, A. / Nango, E. / Nakane, T. / Tanaka, T. / Arima, T. / Neutze, R. / Iwata, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.9 KB | Display | ![]() |
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PDB format | ![]() | 100.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b6vSC ![]() 5b6wC ![]() 5b6yC ![]() 5b6zC ![]() 5h2hC ![]() 5h2iC ![]() 5h2jC ![]() 5h2kC ![]() 5h2lC ![]() 5h2mC ![]() 5h2nC ![]() 5h2oC ![]() 5h2pC C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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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: 26814.412 Da / Num. of mol.: 1 / Fragment: UNP residues 14-261 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700922 / JCM 11081 / NRC-1 / References: UniProt: P02945 |
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-Non-polymers , 11 types, 35 molecules ![](data/chem/img/RET.gif)
![](data/chem/img/L2P.gif)
![](data/chem/img/TRD.gif)
![](data/chem/img/D10.gif)
![](data/chem/img/HP6.gif)
![](data/chem/img/OCT.gif)
![](data/chem/img/MYS.gif)
![](data/chem/img/UND.gif)
![](data/chem/img/DD9.gif)
![](data/chem/img/C14.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/L2P.gif)
![](data/chem/img/TRD.gif)
![](data/chem/img/D10.gif)
![](data/chem/img/HP6.gif)
![](data/chem/img/OCT.gif)
![](data/chem/img/MYS.gif)
![](data/chem/img/UND.gif)
![](data/chem/img/DD9.gif)
![](data/chem/img/C14.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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: 237 % / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2→2.07 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5B6V Resolution: 2.1→21.912 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.97 / 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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