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- PDB-8c87: Double mutant A(L172)C/L(L246)C structure of Photosynthetic React... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c87 | ||||||
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Title | Double mutant A(L172)C/L(L246)C structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV | ||||||
![]() | (Reaction center protein ...) x 3 | ||||||
![]() | PHOTOSYNTHESIS / Photosynthetic reaction center / bacteriochlorophyll / Rhodobacter sphaeroides / spheroidene / ubiquinone / disulfide bond | ||||||
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. / Selikhanov, G. / Fufina, T. / Vasilieva, L. / Atamas, A. / Yukhimchuk, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Stabilization of Cereibacter sphaeroides Photosynthetic Reaction Center by the Introduction of Disulfide Bonds. Authors: Selikhanov, G. / Atamas, A. / Yukhimchuk, D. / Fufina, T. / Vasilieva, L. / Gabdulkhakov, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.3 KB | Display | ![]() |
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PDB format | ![]() | 158 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 42.4 KB | Display | |
Data in CIF | ![]() | 54 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c5xC ![]() 8c6kC ![]() 8c7cC ![]() 8c88C 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: 27189.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: RV / Gene: puhA / Production host: ![]() |
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#2: Protein | Mass: 31382.463 Da / Num. of mol.: 1 / Mutation: S178T, A172C, L246C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: RV / Gene: pufL / Production host: ![]() |
#3: Protein | Mass: 34017.117 Da / Num. of mol.: 1 / Mutation: S8T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: RV / Gene: pufM / Production host: ![]() |
-Non-polymers , 12 types, 94 molecules ![](data/chem/img/LDA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-LDA / #5: Chemical | ChemComp-UNL / Num. of mol.: 5 / Source method: obtained synthetically #6: Chemical | #7: Chemical | ChemComp-OLC / ( | #8: Chemical | ChemComp-BCL / #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-CDL / | #12: Chemical | ChemComp-FE / | #13: Chemical | ChemComp-U10 / | #14: Chemical | ChemComp-SPN / | #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 | Density Matthews: 3.21 Å3/Da / Density % sol: 61.69 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1-mono-oleyl-rac-glycerol (MO), 1,2,3-heptanetriol, Jeffamine M600, N,N-dimethyldodecylamine-N-oxide (LDAO) |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 53136 / % possible obs: 97.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.92 Å2 / CC1/2: 0.96 / Rrim(I) all: 0.11 / Net I/σ(I): 8.26 |
Reflection shell | Resolution: 2.3→2.4 Å / Num. unique obs: 5315 / CC1/2: 0.6 / Rrim(I) all: 0.6 / % possible all: 82.7 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→23.45 Å
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Refine LS restraints |
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LS refinement shell |
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