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- PDB-7vj5: class II photolyase MmCPDII oxidized to semiquinone TR-SFX studie... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vj5 | |||||||||
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Title | class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (5 ms 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209.9 KB | Display | ![]() |
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PDB format | ![]() | 163.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7f8tC ![]() 7viwC ![]() 7vixC ![]() 7viyC ![]() 7vizC ![]() 7vj0C ![]() 7vj1C ![]() 7vj2C ![]() 7vj3C ![]() 7vj4C ![]() 7vj6C ![]() 7vj7C ![]() 7vj8C ![]() 7vj9C ![]() 7vjaC ![]() 7vjbC ![]() 7vjcC ![]() 7vjeC ![]() 7vjgC ![]() 7vjhC ![]() 7vjiC ![]() 7vjjC ![]() 7vjkC ![]() 6lm4 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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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 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.83 % |
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Crystal grow | Temperature: 278 K / Method: batch mode / Details: 0.5-0.65 M Li2SO4 10-15% (W/V) PEG8000 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MPCCD / Detector: CCD / Date: May 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→35.51 Å / Num. obs: 54525 / % possible obs: 100 % / Redundancy: 778.2 % / CC1/2: 0.994 / Net I/σ(I): 7.83 |
Reflection shell | Resolution: 1.85→1.87 Å / Mean I/σ(I) obs: 0.74 / Num. unique obs: 2653 / CC1/2: 0.523 / % possible all: 100 |
Serial crystallography measurement | Focal spot size: 1.77 µm2 / Pulse duration: 10 fsec. / Pulse energy: 10 µJ / Pulse photon energy: 7 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 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LM4 ![]() 6lm4 Resolution: 1.87→35.51 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 33.4 / 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: 1.87→35.51 Å
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Refine LS restraints |
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LS refinement shell |
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