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Yorodumi- PDB-7vjj: class II photolyase MmCPDII semiquinone to fully reduced TR-SFX s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vjj | |||||||||
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Title | class II photolyase MmCPDII semiquinone to fully reduced TR-SFX studies (30 us time-point) | |||||||||
Components | DNA photolyase | |||||||||
Keywords | FLAVOPROTEIN / photolyase / electron transport / photoreduction / time-resolved serial crystallography. | |||||||||
Function / homology | Function and homology information deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / DNA repair / nucleotide binding / DNA binding Similarity search - Function | |||||||||
Biological species | Methanosarcina mazei Go1 (archaea) | |||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | 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 | Japan, 2items
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Citation | Journal: Nat.Chem. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vjj.cif.gz | 207.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vjj.ent.gz | 160.7 KB | Display | PDB format |
PDBx/mmJSON format | 7vjj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vjj_validation.pdf.gz | 943.9 KB | Display | wwPDB validaton report |
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Full document | 7vjj_full_validation.pdf.gz | 953 KB | Display | |
Data in XML | 7vjj_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 7vjj_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/7vjj ftp://data.pdbj.org/pub/pdb/validation_reports/vj/7vjj | HTTPS FTP |
-Related structure data
Related structure data | 7f8tC 7viwC 7vixC 7viyC 7vizC 7vj0C 7vj1C 7vj2C 7vj3C 7vj4C 7vj5C 7vj6C 7vj7C 7vj8C 7vj9C 7vjaC 7vjbC 7vjcC 7vjeC 7vjgC 7vjhC 7vjiC 7vjkC 6lmm C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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.) Methanosarcina mazei Go1 (archaea) / Strain: Go1 / Gene: MM_0852 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q8PYK9, deoxyribodipyrimidine photo-lyase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Chemical | ChemComp-DTT / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.4 % |
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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 |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å |
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: 724.85 % / CC1/2: 0.9941 / Net I/σ(I): 6.65 |
Reflection shell | Resolution: 1.9→1.92 Å / Redundancy: 153.9 % / Mean I/σ(I) obs: 0.87 / Num. unique obs: 2431 / CC1/2: 0.638 / % possible all: 100 |
Serial crystallography measurement | Focal spot size: 1.77 µm2 / Pulse duration: 10 fsec. / Pulse photon energy: 10 keV |
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: 31087 / Frames indexed: 26045 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LMM 6lmm Resolution: 2.1→31.68 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.14 / 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: 2.1→31.68 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 19.4126 Å / Origin y: 24.9988 Å / Origin z: 106.1502 Å
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Refinement TLS group | Selection details: all |