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Yorodumi- PDB-5h2k: A three dimensional movie of structural changes in bacteriorhodop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h2k | ||||||
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Title | A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 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 NRC-1 (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 | 5h2k.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h2k.ent.gz | 101.3 KB | Display | PDB format |
PDBx/mmJSON format | 5h2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h2k_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5h2k_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5h2k_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 5h2k_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/5h2k ftp://data.pdbj.org/pub/pdb/validation_reports/h2/5h2k | HTTPS FTP |
-Related structure data
Related structure data | 5b6vSC 5b6wC 5b6xC 5b6yC 5b6zC 5h2hC 5h2iC 5h2jC 5h2lC 5h2mC 5h2nC 5h2oC 5h2pC S: Starting model for refinement C: citing same article (ref.) |
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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 NRC-1 (Halophile) / Strain: NRC-1 / References: UniProt: P02945 |
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-Non-polymers , 11 types, 35 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 / | |
-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 / pH: 5.4 / 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 5, 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→38.92 Å / Num. obs: 14513 / % possible obs: 100 % / Redundancy: 256 % / CC1/2: 0.99 / Net I/σ(I): 9.24 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B6V Resolution: 2.1→21.912 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
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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