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- PDB-8c3f: Double mutant I(L177)H/F(M197)H structure of Photosynthetic React... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c3f | ||||||
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Title | Double mutant I(L177)H/F(M197)H structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV | ||||||
![]() | (Reaction center protein ...) x 3 | ||||||
![]() | PHOTOSYNTHESIS / Photosynthetic reaction center / bacteriochlorophyll / Rhodobacter sphaeroides / 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. / Fufina, T.Y. / Vasilieva, L.G. | ||||||
Funding support | 1items
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![]() | ![]() Title: Properties and Crystal Structure of the Cereibacter sphaeroides Photosynthetic Reaction Center with Double Amino Acid Substitution I(L177)H + F(M197)H. Authors: Fufina, T.Y. / Selikhanov, G.K. / Gabdulkhakov, A.G. / 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 | ![]() | 225.9 KB | Display | ![]() |
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PDB format | ![]() | 159.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 41.9 KB | Display | |
Data in CIF | ![]() | 52.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v3zS 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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Unit cell |
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Components
-Reaction center protein ... , 3 types, 3 molecules LMH
#1: Protein | Mass: 31385.404 Da / Num. of mol.: 1 / Mutation: S178T, I177H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pufL / Production host: ![]() |
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#2: Protein | Mass: 34008.090 Da / Num. of mol.: 1 / Mutation: S8T, F197H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pufM / Production host: ![]() |
#3: Protein | Mass: 26197.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: puhA / Production host: ![]() |
-Non-polymers , 16 types, 148 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/DIO.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DIO.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-DIO / | #6: Chemical | #7: Chemical | ChemComp-BCL / #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-GOL / | #12: Chemical | ChemComp-LDA / #13: Chemical | ChemComp-FE / | #14: Chemical | ChemComp-SPN / | #15: Chemical | #16: Chemical | ChemComp-CL / | #17: Chemical | ChemComp-CDL / | #18: Chemical | ChemComp-TRS / | #19: 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: 5.65 Å3/Da / Density % sol: 78.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 3.5% 1,2,3 -heptanetriol, 2% dioxane, 0.1% LDAO, 1M potassium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03312 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 64208 / % possible obs: 99.7 % / Redundancy: 9.9 % / Biso Wilson estimate: 63.04 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.6→2.67 Å / Rmerge(I) obs: 2.16 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 4564 / CC1/2: 0.97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3V3Z Resolution: 2.6→46.12 Å / SU ML: 0.3888 / Cross valid method: FREE R-VALUE / σ(F): 0.23 / Phase error: 26.631 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: 64.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→46.12 Å
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Refine LS restraints |
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LS refinement shell |
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