[English] 日本語
![](img/lk-miru.gif)
- PDB-7od5: F(M197)H mutant structure of Photosynthetic Reaction Center From ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7od5 | ||||||
---|---|---|---|---|---|---|---|
Title | F(M197)H mutant structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV LSP crystallization | ||||||
![]() | (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. / Fufina, T.Y. / Vasilieva, L.G. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: X-ray structure of the Rhodobacter sphaeroides reaction center with an M197 Phe→His substitution clarifies the properties of the mutant complex. Authors: Selikhanov, G. / Fufina, T. / Guenther, S. / Meents, A. / Gabdulkhakov, A. / Vasilieva, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 228.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 161.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 37.3 KB | Display | |
Data in CIF | ![]() | 51.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p2cC ![]() 6z1jS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
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.) ![]() ![]() |
---|---|
#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, 251 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/FE.gif)
![](data/chem/img/U10.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/FE.gif)
![](data/chem/img/U10.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.: 4 / Source method: obtained synthetically #6: Chemical | ChemComp-OLC / ( | #7: Chemical | ChemComp-BCL / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-FE / | #11: Chemical | ChemComp-U10 / | #12: Chemical | ChemComp-SPN / | #13: Chemical | ChemComp-EDO / | #14: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.2 % |
---|---|
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: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 71237 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 38.85 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.93 |
Reflection shell | Resolution: 2.1→2.23 Å / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 11313 / CC1/2: 0.69 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6Z1J Resolution: 2.1→46.09 Å / SU ML: 0.2153 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.2158 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.09 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|