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- PDB-7p0q: F(M197)H mutant structure of Photosynthetic Reaction Center From ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p0q | ||||||
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Title | F(M197)H mutant structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV by fixed-target serial synchrotron crystallography (100K, 26keV) | ||||||
![]() | (Reaction center protein ...) x 3 | ||||||
![]() | PHOTOSYNTHESIS / Photosynthetic reaction center / bacteriochlorophyll / Rhodobacter sphaeroides / serial crystallography / mesophase crystallization / lipid sponge phase / lipid cubic phase / spheroidene / ubiquinone | ||||||
Function / homology | ![]() plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gabdulkhakov, A.G. / Selikhanov, G.K. / Guenther, S. / Meents, A. / Fufina, T.Y. / Vasilieva, L.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: X-Ray structure of Rhodobacter sphaeroides reaction center with M197 Phe-His substitution clarifies properties of the mutant complex 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 | ![]() | 229.9 KB | Display | ![]() |
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PDB format | ![]() | 161.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 40.2 KB | Display | |
Data in CIF | ![]() | 55.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p17C ![]() 6z1jS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
-Reaction center protein ... , 3 types, 3 molecules HLM
#1: Protein | Mass: 26197.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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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.) ![]() ![]() |
#3: Protein | Mass: 34008.090 Da / Num. of mol.: 1 / Mutation: S8T, F197H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 11 types, 408 molecules ![](data/chem/img/LDA.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.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/HOH.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.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/HOH.gif)
#4: Chemical | ChemComp-LDA / #5: Chemical | ChemComp-UNL / Num. of mol.: 7 / Source method: obtained synthetically #6: Chemical | ChemComp-OLC / ( | #7: Chemical | ChemComp-BCL / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-U10 / | #11: Chemical | ChemComp-FE / | #12: Chemical | ChemComp-SPN / | #13: Chemical | ChemComp-EDO / | #14: 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: 3.25 Å3/Da / Density % sol: 62.2 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 1-mono-oleyl-rac-glycerol (MO), 1,2,3-heptanetriol, Jeffamine M600, N,N-dimethyldodecylamine-N-oxide (LDAO) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.4769 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→49 Å / Num. obs: 126837 / % possible obs: 100 % / Redundancy: 68.3 % / Biso Wilson estimate: 32.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.028 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 63.6 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6215 / CC1/2: 0.3 / % possible all: 99.9 |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography sample delivery fixed target | Sample holding: silicon chip / Support base: Roadruner |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6z1j Resolution: 1.73→48.93 Å / SU ML: 0.2433 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.5991 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: 35.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→48.93 Å
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Refine LS restraints |
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LS refinement shell |
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