[English] 日本語
![](img/lk-miru.gif)
- PDB-5mjp: Multi-bunch pink beam serial crystallography: Phycocyanin (One chip) -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5mjp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Multi-bunch pink beam serial crystallography: Phycocyanin (One chip) | |||||||||
![]() |
| |||||||||
![]() | PHOTOSYNTHESIS / Phycocyanin / Serial Crystallography / Pink beam | |||||||||
Function / homology | ![]() phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Meents, A. / Oberthuer, D. / Lieske, J. / Srajer, V. / Sarrou, I. | |||||||||
![]() | ![]() Title: Pink-beam serial crystallography. Authors: Meents, A. / Wiedorn, M.O. / Srajer, V. / Henning, R. / Sarrou, I. / Bergtholdt, J. / Barthelmess, M. / Reinke, P.Y.A. / Dierksmeyer, D. / Tolstikova, A. / Schaible, S. / Messerschmidt, M. / ...Authors: Meents, A. / Wiedorn, M.O. / Srajer, V. / Henning, R. / Sarrou, I. / Bergtholdt, J. / Barthelmess, M. / Reinke, P.Y.A. / Dierksmeyer, D. / Tolstikova, A. / Schaible, S. / Messerschmidt, M. / Ogata, C.M. / Kissick, D.J. / Taft, M.H. / Manstein, D.J. / Lieske, J. / Oberthuer, D. / Fischetti, R.F. / Chapman, H.N. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 202.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 167.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5mjlC ![]() 5mjmC ![]() 5mjqC ![]() 5o7mC ![]() 1jboS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 6||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 17456.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P50032 | ||
---|---|---|---|
#2: Protein | Mass: 18216.652 Da / Num. of mol.: 1 / Mutation: N73X / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P50033 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.36 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: Ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 293 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Jul 10, 2016 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2.106→14.92 Å / Num. obs: 15458 / % possible obs: 64.7 % / Redundancy: 1 % / Biso Wilson estimate: 15.21 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 31.68 | |||||||||
Reflection shell | Resolution: 2.12→2.22 Å / Num. unique all: 759 / Num. unique obs: 9048 / % possible all: 26.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1JBO Resolution: 2.11→14.9 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.7 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→14.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|