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- PDB-6zid: Ultrafast Structural Response to Charge Redistribution Within a P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zid | ||||||||||||||||||
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Title | Ultrafast Structural Response to Charge Redistribution Within a Photosynthetic Reaction Centre - 5 ps (b) structure | ||||||||||||||||||
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Function / homology | ![]() plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Baath, P. / Dods, R. / Braenden, G. / Neutze, R. | ||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Ultrafast structural changes within a photosynthetic reaction centre. Authors: Dods, R. / Bath, P. / Morozov, D. / Gagner, V.A. / Arnlund, D. / Luk, H.L. / Kubel, J. / Maj, M. / Vallejos, A. / Wickstrand, C. / Bosman, R. / Beyerlein, K.R. / Nelson, G. / Liang, M. / ...Authors: Dods, R. / Bath, P. / Morozov, D. / Gagner, V.A. / Arnlund, D. / Luk, H.L. / Kubel, J. / Maj, M. / Vallejos, A. / Wickstrand, C. / Bosman, R. / Beyerlein, K.R. / Nelson, G. / Liang, M. / Milathianaki, D. / Robinson, J. / Harimoorthy, R. / Berntsen, P. / Malmerberg, E. / Johansson, L. / Andersson, R. / Carbajo, S. / Claesson, E. / Conrad, C.E. / Dahl, P. / Hammarin, G. / Hunter, M.S. / Li, C. / Lisova, S. / Royant, A. / Safari, C. / Sharma, A. / Williams, G.J. / Yefanov, O. / Westenhoff, S. / Davidsson, J. / DePonte, D.P. / Boutet, S. / Barty, A. / Katona, G. / Groenhof, G. / Branden, G. / Neutze, R. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 346.7 KB | Display | ![]() |
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PDB format | ![]() | 243.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zhwC ![]() 6zi4C ![]() 6zi5C ![]() 6zi6C ![]() 6zi9C ![]() 6ziaC ![]() 2i5nS 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules C
#1: Protein | Mass: 37450.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Reaction center protein ... , 3 types, 3 molecules HLM
#2: Protein | ![]() Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Protein | ![]() Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | ![]() Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 11 types, 185 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/BCB.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MQ7.gif)
![](data/chem/img/NS5.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/BCB.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MQ7.gif)
![](data/chem/img/NS5.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-HEC / ![]() #6: Chemical | ChemComp-DGA / | ![]() #7: Chemical | ChemComp-SO4 / ![]() #8: Chemical | ChemComp-LDA / ![]() #9: Chemical | #10: Chemical | ChemComp-BCB / ![]() #11: Chemical | ![]() #12: Chemical | ChemComp-FE / | ![]() #13: Chemical | ChemComp-MQ7 / | ![]() #14: Chemical | ChemComp-NS5 / | #15: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Macrocrystal growth: 10 mg/ml protein, 3.6 M ammonium sulphate, 6 % w/v heptane-1,2,3-triol, 20 mM KH203/K2H03 pH 6.8, 0.1 % LDAO 20 ul sitting drop, 10 protein : 10 precipitant ...Details: Macrocrystal growth: 10 mg/ml protein, 3.6 M ammonium sulphate, 6 % w/v heptane-1,2,3-triol, 20 mM KH203/K2H03 pH 6.8, 0.1 % LDAO 20 ul sitting drop, 10 protein : 10 precipitant Microcrystals: 8.5 mg/ml protein 18.5 ul sitting drop, 10 protein : 7.5 precipitant : 1 seed stock |
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-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Jun 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→35.8 Å / Num. obs: 75091 / % possible obs: 100 % / Redundancy: 5350 % / Biso Wilson estimate: 98.13 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.42 |
Reflection shell | Resolution: 2.8→2.83 Å / Mean I/σ(I) obs: 2.33 / Num. unique obs: 4961 / CC1/2: 0.908 |
Serial crystallography sample delivery | Method: injection |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2I5N Resolution: 2.8→34.31 Å / SU ML: 0.2699 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7647 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→34.31 Å
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Refine LS restraints |
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LS refinement shell |
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