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- PDB-5m7j: Blastochloris viridis photosynthetic reaction center structure us... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m7j | ||||||
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Title | Blastochloris viridis photosynthetic reaction center structure using best crystal approach | ||||||
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Function / homology | ![]() plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharma, A.S. / Johansson, L. / Dunevall, E. / Wahlgren, W.Y. / Neutze, R. / Katona, G. | ||||||
![]() | ![]() Title: Asymmetry in serial femtosecond crystallography data. Authors: Sharma, A. / Johansson, L. / Dunevall, E. / Wahlgren, W.Y. / Neutze, R. / Katona, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 273.6 KB | Display | ![]() |
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PDB format | ![]() | 212.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5m7kC ![]() 5m7lC ![]() 4casS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39419.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Reaction center protein ... , 3 types, 3 molecules BCD
#2: Protein | ![]() Mass: 30600.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Protein | ![]() Mass: 36063.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | ![]() Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 10 types, 20 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/MPG.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/MQ7.gif)
![](data/chem/img/NS5.gif)
![](data/chem/img/OTP.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/MPG.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/MQ7.gif)
![](data/chem/img/NS5.gif)
![](data/chem/img/OTP.gif)
![](data/chem/img/PO4.gif)
#5: Chemical | ChemComp-HEC / ![]() #6: Chemical | ChemComp-DGA / | ![]() #7: Chemical | ChemComp-BCL / ![]() #8: Chemical | ![]() #9: Chemical | #10: Chemical | ChemComp-FE2 / | #11: Chemical | ChemComp-MQ7 / | ![]() #12: Chemical | ChemComp-NS5 / | #13: Chemical | ChemComp-OTP / ( | #14: Chemical | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.95 % |
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Crystal grow![]() | Temperature: 293 K / Method: batch mode Details: Melted monoolein was thoroughly mixed in a ratio of 3:2 (v/v) with 0.1M HEPES, pH 7.5, 0.1 % LDAO until a viscous, transparent LCP was obtained. The formed phase was then transferred into a ...Details: Melted monoolein was thoroughly mixed in a ratio of 3:2 (v/v) with 0.1M HEPES, pH 7.5, 0.1 % LDAO until a viscous, transparent LCP was obtained. The formed phase was then transferred into a glass vial and sponge-phase-inducing solution (1:4 ratio) was added containing 16% Jeffamine M-600, 1M HEPES pH 7.9, 0.7 M Ammonium sulphate, 2.5% 1,2,3-Heptanetriol, which swell the cubic phase to sponge phase. After phase separation overnight, the upper phase (sponge phase) was harvested. Crystals were grown using batch crystallization in the lipidic-sponge phase. Equal amount of sponge phase and protein were mixed with 2/5 (v/v) of 1.2 M Tris-sodium citrate and allowed to incubate for several weeks. |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.5→58 Å / Num. obs: 24815 / % possible obs: 99.4 % / Redundancy: 59 % / Net I/σ(I): 6.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4CAS Resolution: 3.5→52.761 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→52.761 Å
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Refine LS restraints |
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LS refinement shell |
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