[English] 日本語
![](img/lk-miru.gif)
- PDB-6z27: Photosynthetic Reaction Center From Rhodobacter Sphaeroides strai... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6z27 | ||||||
---|---|---|---|---|---|---|---|
Title | Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV LCP 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. / Fufina, T.Y. / Vasilieva, L.G. / Betzel, C. / Selikhanov, G.K. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Novel approaches for the lipid sponge phase crystallization of the Rhodobacter sphaeroides photosynthetic reaction center. Authors: Selikhanov, G. / Fufina, T. / Vasilieva, L. / Betzel, C. / Gabdulkhakov, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 217 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 154.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6z02C ![]() 6z1jC ![]() 3v3yS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
-Reaction center protein ... , 3 types, 3 molecules HLM
#1: Protein | Mass: 27047.104 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: 33885.922 Da / Num. of mol.: 1 / Mutation: S8T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 9 types, 187 molecules ![](data/chem/img/LDA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-LDA / #5: Chemical | ChemComp-PO4 / #6: Chemical | #7: Chemical | ChemComp-BCL / #8: Chemical | #9: Chemical | ChemComp-FE / | #10: Chemical | ChemComp-U10 / | #11: Chemical | ChemComp-EDO / | #12: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.13 % |
---|---|
Crystal grow | Temperature: 289 K / Method: batch mode 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 6M / Detector: PIXEL / Date: Jun 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.861 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. obs: 72564 / % possible obs: 99.9 % / Redundancy: 11.06 % / Biso Wilson estimate: 52.2 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.94 |
Reflection shell | Resolution: 2.07→2.13 Å / Mean I/σ(I) obs: 1.14 / Num. unique obs: 5862 / CC1/2: 0.31 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3V3Y Resolution: 2.1→48.86 Å / SU ML: 0.2725 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.4563 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: 59.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→48.86 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|