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- PDB-7z8d: Structure of Photosynthetic Reaction Center From Rhodobacter Spha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z8d | ||||||
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Title | Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV by fixed-target serial synchrotron crystallography (room temperature, 26keV) | ||||||
![]() | (Reaction center protein ...![]() | ||||||
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Function / homology | ![]() plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gabdulkhakov, A.G. / Selikhanov, G.K. / Guenther, S. / Petrova, T. / Meents, A. / Fufina, T.Y. / Vasilieva, L.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV by fixed-target serial synchrotron crystallography (room temperature, 26keV) Authors: Gabdulkhakov, A.G. / Selikhanov, G.K. / Guenther, S. / Meents, A. / Fufina, T.Y. / Vasilieva, L.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229 KB | Display | ![]() |
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PDB format | ![]() | 161.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6z1jS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Reaction center protein ... , 3 types, 3 molecules HLM
#1: Protein | ![]() Mass: 26284.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: puhA / Production host: ![]() |
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#2: Protein | ![]() Mass: 31360.416 Da / Num. of mol.: 1 / Mutation: S178T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pufL / Production host: ![]() |
#3: Protein | ![]() Mass: 33885.922 Da / Num. of mol.: 1 / Mutation: S8T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pufM / Production host: ![]() |
-Non-polymers , 13 types, 201 molecules ![](data/chem/img/LDA.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/D12.gif)
![](data/chem/img/MYS.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/NKP.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/D12.gif)
![](data/chem/img/MYS.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/NKP.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-LDA / ![]() #5: Chemical | ChemComp-BCL / ![]() #6: Chemical | ![]() #7: Chemical | ![]() #8: Chemical | ChemComp-MYS / | ![]() #9: Chemical | ChemComp-OLC / ( | #10: Chemical | #11: Chemical | ChemComp-U10 / | ![]() #12: Chemical | ChemComp-FE / | ![]() #13: Chemical | ChemComp-SPN / | #14: Chemical | ChemComp-EDO / | ![]() #15: Chemical | ChemComp-PO4 / | ![]() #16: 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 | Density Matthews: 3.41 Å3/Da / Density % sol: 63.89 % |
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Crystal grow![]() | Temperature: 289 K / Method: small tubes Details: 1-mono-oleyl-rac-glycerol (MO), 1,2,3-heptanetriol, Jeffamine M600, N,N-dimethyldodecylamine-N-oxide (LDAO) |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Dec 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.14→50 Å / Num. obs: 70474 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 38.14 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.18 / Net I/σ(I): 10.06 |
Reflection shell | Resolution: 2.14→2.2 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 1.38 / Num. unique obs: 5099 / CC1/2: 0.54 / Rrim(I) all: 1.9 / % possible all: 100 |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography sample delivery fixed target | Description: Roadruner / Sample holding: silicon chip |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6z1j Resolution: 2.14→47.05 Å / SU ML: 0.2604 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7241 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: 41.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→47.05 Å
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Refine LS restraints |
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LS refinement shell |
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