[English] 日本語
![](img/lk-miru.gif)
- PDB-7vjb: class II photolyase MmCPDII semiquinone to fully reduced TR-SFX s... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7vjb | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | class II photolyase MmCPDII semiquinone to fully reduced TR-SFX studies (30 ns time-point) | |||||||||
![]() | DNA photolyase | |||||||||
![]() | FLAVOPROTEIN / photolyase / electron transport / photoreduction / time-resolved serial crystallography. | |||||||||
Function / homology | ![]() photoreactive repair / deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / nucleotide binding / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Maestre-Reyna, M. / Yang, C.-H. / Huang, W.-C. / Nango, E. / Ngura Putu, E.P.G. / Franz-Badur, S. / Wu, W.-J. / Wu, H.-Y. / Wang, P.-H. / Hosokawa, Y. ...Maestre-Reyna, M. / Yang, C.-H. / Huang, W.-C. / Nango, E. / Ngura Putu, E.P.G. / Franz-Badur, S. / Wu, W.-J. / Wu, H.-Y. / Wang, P.-H. / Hosokawa, Y. / Saft, M. / Emmerich, H.-J. / Liao, J.-H. / Lee, C.-C. / Huang, K.-F. / Chang, Y.-K. / Weng, J.-H. / Royant, A. / Gad, W. / Pang, A.H. / Chang, C.-W. / Sugahara, M. / Owada, S. / Joti, Y. / Yamashita, A. / Tanaka, R. / Tanaka, T. / Luo, F.J. / Tono, K. / Kiontke, S. / Yamamoto, J. / Iwata, S. / Essen, L.-O. / Bessho, Y. / Tsai, M.-D. | |||||||||
Funding support | ![]() ![]()
| |||||||||
![]() | ![]() Title: Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme. Authors: Maestre-Reyna, M. / Yang, C.H. / Nango, E. / Huang, W.C. / Ngurah Putu, E.P.G. / Wu, W.J. / Wang, P.H. / Franz-Badur, S. / Saft, M. / Emmerich, H.J. / Wu, H.Y. / Lee, C.C. / Huang, K.F. / ...Authors: Maestre-Reyna, M. / Yang, C.H. / Nango, E. / Huang, W.C. / Ngurah Putu, E.P.G. / Wu, W.J. / Wang, P.H. / Franz-Badur, S. / Saft, M. / Emmerich, H.J. / Wu, H.Y. / Lee, C.C. / Huang, K.F. / Chang, Y.K. / Liao, J.H. / Weng, J.H. / Gad, W. / Chang, C.W. / Pang, A.H. / Sugahara, M. / Owada, S. / Hosokawa, Y. / Joti, Y. / Yamashita, A. / Tanaka, R. / Tanaka, T. / Luo, F. / Tono, K. / Hsu, K.C. / Kiontke, S. / Schapiro, I. / Spadaccini, R. / Royant, A. / Yamamoto, J. / Iwata, S. / Essen, L.O. / Bessho, Y. / Tsai, M.D. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 130.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 84.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7f8tC ![]() 7viwC ![]() 7vixC ![]() 7viyC ![]() 7vizC ![]() 7vj0C ![]() 7vj1C ![]() 7vj2C ![]() 7vj3C ![]() 7vj4C ![]() 7vj5C ![]() 7vj6C ![]() 7vj7C ![]() 7vj8C ![]() 7vj9C ![]() 7vjaC ![]() 7vjcC ![]() 7vjeC ![]() 7vjgC ![]() 7vjhC ![]() 7vjiC ![]() 7vjjC ![]() 7vjkC ![]() 6lmm C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 55123.480 Da / Num. of mol.: 1 / Mutation: M377T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8PYK9, deoxyribodipyrimidine photo-lyase | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Chemical | ChemComp-DTT / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.69 % |
---|---|
Crystal grow | Temperature: 277 K / Method: microbatch / Details: 0.5-0.65 M Li2SO4 10-15% (W/V) PEG8000 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MPCCD / Detector: CCD / Date: Feb 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→33.9 Å / Num. obs: 50254 / % possible obs: 100 % / Redundancy: 716.66 % / Biso Wilson estimate: 40.87 Å2 / CC1/2: 0.99638 / Net I/σ(I): 7.39 |
Reflection shell | Resolution: 1.9→1.92 Å / Mean I/σ(I) obs: 0.98 / Num. unique obs: 2431 / CC1/2: 0.69 / % possible all: 100 |
Serial crystallography measurement | Focal spot size: 1.77 µm2 / Pulse duration: 10 fsec. / Pulse photon energy: 10 keV / XFEL pulse repetition rate: 30 Hz |
Serial crystallography sample delivery | Description: High viscosity injector / Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: grease / Filter size: 70 µm / Flow rate: 4.5 µL/min / Injector diameter: 100 µm / Injector nozzle: 100 / Injector temperature: 293 K / Jet diameter: 100 µm / Power by: gas |
Serial crystallography data reduction | Crystal hits: 27482 / Frames indexed: 23169 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6LMM ![]() 6lmm Resolution: 2.1→31.68 Å / SU ML: 0.2125 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.638 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: 50.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→31.68 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|