[English] 日本語
![](img/lk-miru.gif)
- PDB-7q7q: LIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7q7q | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | LIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE OF A PHOTOSYNTHETIC REACTION CENTRE | |||||||||
![]() |
| |||||||||
![]() | MEMBRANE PROTEIN / CRYSTALLOGRAPHY STRUCTURE PHOTOSYNTHETIC REACTION CENTRE | |||||||||
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 / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Baath, P. / Banacore, A. / Neutze, R. | |||||||||
Funding support | European Union, ![]()
| |||||||||
![]() | ![]() Title: Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre. Authors: Bath, P. / Banacore, A. / Borjesson, P. / Bosman, R. / Wickstrand, C. / Safari, C. / Dods, R. / Ghosh, S. / Dahl, P. / Ortolani, G. / Bjorg Ulfarsdottir, T. / Hammarin, G. / Garcia Bonete, M. ...Authors: Bath, P. / Banacore, A. / Borjesson, P. / Bosman, R. / Wickstrand, C. / Safari, C. / Dods, R. / Ghosh, S. / Dahl, P. / Ortolani, G. / Bjorg Ulfarsdottir, T. / Hammarin, G. / Garcia Bonete, M.J. / Vallejos, A. / Ostojic, L. / Edlund, P. / Linse, J.B. / Andersson, R. / Nango, E. / Owada, S. / Tanaka, R. / Tono, K. / Joti, Y. / Nureki, O. / Luo, F. / James, D. / Nass, K. / Johnson, P.J.M. / Knopp, G. / Ozerov, D. / Cirelli, C. / Milne, C. / Iwata, S. / Branden, G. / Neutze, R. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 297.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 5.5 MB | Display | |
Data in XML | ![]() | 35.5 KB | Display | |
Data in CIF | ![]() | 49.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q7pC ![]() 5nj4S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules CCC
#1: Protein | Mass: 37450.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|
-Reaction center protein ... , 3 types, 3 molecules HHHLLLMMM
#2: Protein | Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#3: Protein | Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 13 types, 305 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BCB.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/UQ2.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/MQ9.gif)
![](data/chem/img/NS5.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BCB.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/UQ2.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/MQ9.gif)
![](data/chem/img/NS5.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-DGA / | #7: Chemical | ChemComp-LDA / #8: Chemical | ChemComp-SO4 / #9: Chemical | ChemComp-BCB / #10: Chemical | #11: Chemical | ChemComp-HTO / #12: Chemical | #13: Chemical | ChemComp-FE2 / | #14: Chemical | ChemComp-MQ9 / | #15: Chemical | ChemComp-NS5 / | #16: Chemical | #17: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.28 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: This LCP crystallization was performed in wells with 200uL precipitant and 20uL LCP+protein. |
-Data collection
Diffraction | Mean temperature: 293 K / Ambient temp details: Room Temperature / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Nov 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.102 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→23.702 Å / Num. obs: 92545 / % possible obs: 100 % / Redundancy: 11.888 % / CC1/2: 0.995 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.25→2.27 Å / Num. unique obs: 92545 / CC1/2: 0.54 |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Flow rate: 0.047 µL/min / Injector diameter: 75 µm / Injector temperature: 293 K |
Serial crystallography data reduction | Crystal hits: 260392 / Frames indexed: 160275 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5NJ4 Resolution: 2.25→23.702 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.515 / SU ML: 0.126 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.161 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.98 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→23.702 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|