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- PDB-6gaf: BACTERIORHODOPSIN, 590 FS STATE, REAL-SPACE REFINED AGAINST 15% E... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gaf | ||||||
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Title | BACTERIORHODOPSIN, 590 FS STATE, REAL-SPACE REFINED AGAINST 15% EXTRAPOLATED STRUCTURE FACTORS | ||||||
![]() | Bacteriorhodopsin | ||||||
![]() | MEMBRANE PROTEIN / proton pump / time-resolved crystallography / free-electron laser | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
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 | ![]() | 93.8 KB | Display | ![]() |
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PDB format | ![]() | 79.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ga1C ![]() 6ga2C ![]() 6ga3C ![]() 6ga4C ![]() 6ga5C ![]() 6ga6C ![]() 6ga7C ![]() 6ga8C ![]() 6ga9C ![]() 6gaaC ![]() 6gabC ![]() 6gacC ![]() 6gadC ![]() 6gaeC ![]() 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 on special symmetry positions |
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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, 53 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: 2.28 Å3/Da / Density % sol: 46.15 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.8 / 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: 22397 / % possible obs: 100 % / Redundancy: 136 % / R split: 0.12 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.8→1.9 Å / R split: 0.841 |
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Processing
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Refinement | Resolution: 1.8→20 Å / Cross valid method: NONE 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)=0.8347
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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