[English] 日本語
![](img/lk-miru.gif)
- PDB-6z02: Photosynthetic Reaction Center From Rhodobacter Sphaeroides strai... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6z02 | ||||||
---|---|---|---|---|---|---|---|
Title | Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV in surfo 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. / Betzel, C. | ||||||
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 | ![]() | 230.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 172.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 44.6 KB | Display | |
Data in CIF | ![]() | 60.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z1jC ![]() 6z27C ![]() 3v3yS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
-Reaction center protein ... , 3 types, 3 molecules HLM
#1: Protein | Mass: 26170.078 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 33885.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 17 types, 494 molecules ![](data/chem/img/LDA.gif)
![](data/chem/img/D12.gif)
![](data/chem/img/MYS.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/D10.gif)
![](data/chem/img/DIO.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/D12.gif)
![](data/chem/img/MYS.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/D10.gif)
![](data/chem/img/DIO.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-LDA / #5: Chemical | ChemComp-D12 / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-NA / | #10: Chemical | ChemComp-K / | #11: Chemical | ChemComp-BCL / #12: Chemical | #13: Chemical | #14: Chemical | ChemComp-D10 / | #15: Chemical | ChemComp-DIO / | #16: Chemical | #17: Chemical | ChemComp-FE / | #18: Chemical | ChemComp-SPN / | #19: Chemical | ChemComp-CDL / | #20: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.72 Å3/Da / Density % sol: 78.51 % |
---|---|
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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 121690 / % possible obs: 99.5 % / Redundancy: 4.75 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.52 |
Reflection shell | Resolution: 2.1→2.2 Å / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 15297 / CC1/2: 0.36 / % possible all: 96.9 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3V3Y Resolution: 2.1→43.2 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.92 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→43.2 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.13 Å
|