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- PDB-6ga4: Bacteriorhodopsin, 1 ps state, real-space refined against 15% ext... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ga4 | ||||||
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Title | Bacteriorhodopsin, 1 ps state, real-space refined against 15% extrapolated map | ||||||
![]() | Bacteriorhodopsin | ||||||
![]() | MEMBRANE PROTEIN / proton pump / time-resolved crystallography / free-electron laser | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nass Kovacs, G. / Colletier, J.-P. / Gruenbein, M.L. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. ...Nass Kovacs, G. / Colletier, J.-P. / Gruenbein, M.L. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. / Gorel, A. / Hilpert, M. / Kloos, M. / Koglin, J. / Reinstein, J. / Roome, C.M. / Schlesinger, R. / Seaberg, M. / Shoeman, R.L. / Stricker, M. / Boutet, S. / Haacke, S. / Heberle, J. / Domratcheva, T. / Schlichting, I. | ||||||
Funding support | 1items
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![]() | ![]() Title: Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin. Authors: Nass Kovacs, G. / Colletier, J.P. / Grunbein, M.L. / Yang, Y. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. / Gorel, A. / Hilpert, M. / ...Authors: Nass Kovacs, G. / Colletier, J.P. / Grunbein, M.L. / Yang, Y. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. / Gorel, A. / Hilpert, M. / Kloos, M. / Koglin, J.E. / Reinstein, J. / Roome, C.M. / Schlesinger, R. / Seaberg, M. / Shoeman, R.L. / Stricker, M. / Boutet, S. / Haacke, S. / Heberle, J. / Heyne, K. / Domratcheva, T. / Barends, T.R.M. / Schlichting, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.7 KB | Display | ![]() |
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PDB format | ![]() | 79.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ga1C ![]() 6ga2C ![]() 6ga3C ![]() 6ga5C ![]() 6ga6C ![]() 6ga7C ![]() 6ga8C ![]() 6ga9C ![]() 6gaaC ![]() 6gabC ![]() 6gacC ![]() 6gadC ![]() 6gaeC ![]() 6gafC ![]() 6gagC ![]() 6gahC ![]() 6gaiC ![]() 6rmkC C: citing same article ( |
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Similar structure data |
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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: 26929.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700922 / JCM 11081 / NRC-1 / Gene: bop, VNG_1467G / Production host: ![]() |
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-Non-polymers , 11 types, 58 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 | ChemComp-MYS / | #9: Chemical | #10: Chemical | ChemComp-DD9 / | #11: Chemical | ChemComp-C14 / | #12: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.85 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.6 / Details: 32% (w/v) PEG 2000, 0.1 M K2HPO4 /NaH2PO4 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD CXI-2 / Detector: PIXEL / Date: Jul 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.26 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→21 Å / Num. obs: 22376 / % possible obs: 100 % / Redundancy: 231 % / R split: 0.108 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.8→1.9 Å / R split: 0.793 |
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Processing
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Refinement | Resolution: 1.8→20.455 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 0.31 / Phase error: 21.97 Details: A MOLECULE IS THE DARK STATE B MOLECULE WAS REAL-SPACE REFINED AGAINST MAP CALCULATED FROM EXTRAPOLATED STRUCTURE FACTORS (AT 15% OCCUPANCY) MODEL/MAP FIT (CCmask)=0.8408
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20.455 Å
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Refine LS restraints |
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LS refinement shell |
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