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Yorodumi- PDB-7yeb: TR-SFX MmCPDII-DNA complex: 3.35 ns snapshot. Includes 3.35 ns, d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yeb | ||||||||||||
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Title | TR-SFX MmCPDII-DNA complex: 3.35 ns snapshot. Includes 3.35 ns, dark, and extrapolated structure factors | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / Flavoprotein / photolyase / light driven electron transfer / DNA repair / time-resolved serial crystallography. | ||||||||||||
Function / homology | Function and homology information photoreactive repair / deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||||||||
Biological species | Methanosarcina mazei (archaea) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Maestre-Reyna, M. / Wang, P.-H. / Nango, E. / Hosokawa, Y. / Saft, M. / Furrer, A. / Yang, C.-H. / Ngura Putu, E.P.G. / Wu, W.-J. / Emmerich, H.-J. ...Maestre-Reyna, M. / Wang, P.-H. / Nango, E. / Hosokawa, Y. / Saft, M. / Furrer, A. / Yang, C.-H. / Ngura Putu, E.P.G. / Wu, W.-J. / Emmerich, H.-J. / Engilberge, S. / Caramello, N. / Wranik, M. / Glover, H.L. / Franz-Badur, S. / Wu, H.-Y. / Lee, C.-C. / Huang, W.-C. / Huang, K.-F. / Chang, Y.-K. / Liao, J.-H. / Weng, J.-H. / Gad, W. / Chang, C.-W. / Pang, A.H. / Gashi, D. / Beale, E. / Ozerov, D. / Milne, C. / Cirelli, C. / Bacellar, C. / Sugahara, M. / Owada, S. / Joti, Y. / Yamashita, A. / Tanaka, R. / Tanaka, T. / Luo, F.J. / Tono, K. / Kiontke, S. / Spadaccini, R. / Royant, A. / Yamamoto, J. / Iwata, S. / Standfuss, J. / Essen, L.-O. / Bessho, Y. / Tsai, M.-D. | ||||||||||||
Funding support | Taiwan, Japan, 3items
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Citation | Journal: Science / Year: 2023 Title: Visualizing the DNA repair process by a photolyase at atomic resolution. Authors: Maestre-Reyna, M. / Wang, P.H. / Nango, E. / Hosokawa, Y. / Saft, M. / Furrer, A. / Yang, C.H. / Gusti Ngurah Putu, E.P. / Wu, W.J. / Emmerich, H.J. / Caramello, N. / Franz-Badur, S. / Yang, ...Authors: Maestre-Reyna, M. / Wang, P.H. / Nango, E. / Hosokawa, Y. / Saft, M. / Furrer, A. / Yang, C.H. / Gusti Ngurah Putu, E.P. / Wu, W.J. / Emmerich, H.J. / Caramello, N. / Franz-Badur, S. / Yang, C. / Engilberge, S. / Wranik, M. / Glover, H.L. / Weinert, T. / Wu, H.Y. / Lee, C.C. / Huang, W.C. / Huang, K.F. / Chang, Y.K. / Liao, J.H. / Weng, J.H. / Gad, W. / Chang, C.W. / Pang, A.H. / Yang, K.C. / Lin, W.T. / Chang, Y.C. / Gashi, D. / Beale, E. / Ozerov, D. / Nass, K. / Knopp, G. / Johnson, P.J.M. / Cirelli, C. / Milne, C. / Bacellar, C. / Sugahara, M. / Owada, S. / Joti, Y. / Yamashita, A. / Tanaka, R. / Tanaka, T. / Luo, F. / Tono, K. / Zarzycka, W. / Muller, P. / Alahmad, M.A. / Bezold, F. / Fuchs, V. / Gnau, P. / Kiontke, S. / Korf, L. / Reithofer, V. / Rosner, C.J. / Seiler, E.M. / Watad, M. / Werel, L. / Spadaccini, R. / Yamamoto, J. / Iwata, S. / Zhong, D. / Standfuss, J. / Royant, A. / Bessho, Y. / Essen, L.O. / 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 | 7yeb.cif.gz | 430.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yeb.ent.gz | 342.5 KB | Display | PDB format |
PDBx/mmJSON format | 7yeb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yeb_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7yeb_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7yeb_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 7yeb_validation.cif.gz | 55.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/7yeb ftp://data.pdbj.org/pub/pdb/validation_reports/ye/7yeb | HTTPS FTP |
-Related structure data
Related structure data | 7yc7SC 7ycmC 7ycpC 7ycrC 7yd6C 7yd7C 7yd8C 7ydzC 7ye0C 7yecC 7yeeC 7yeiC 7yejC 7yekC 7yelC 7yemC 8kcmC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-CPD photolesion containing ... , 2 types, 2 molecules CE
#2: DNA chain | Mass: 4569.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 4569.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein / DNA chain , 2 types, 4 molecules ABDF
#1: Protein | Mass: 55123.480 Da / Num. of mol.: 2 / Mutation: M377T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F8I5V2 #3: DNA chain | Mass: 4305.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 375 molecules
#5: Chemical | ChemComp-SO4 / | ||
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#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.74 % |
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Crystal grow | Temperature: 296 K / Method: batch mode / pH: 4.6 Details: 100 mM Sodium Acetate pH 4.6 250 mM ammonium sulfate 4% PEG4000 (w/v) 50 mM DTT |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.0875 Å |
Detector | Type: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Sep 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0875 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→16.74 Å / Num. obs: 81528 / % possible obs: 99.99 % / Redundancy: 1073.4 % / CC1/2: 0.996 / Net I/σ(I): 11.09 |
Reflection shell | Resolution: 2.12→2.14 Å / Redundancy: 577.9 % / Mean I/σ(I) obs: 1.99 / Num. unique obs: 4004 / CC1/2: 0.565 / % possible all: 100 |
Serial crystallography measurement | XFEL pulse repetition rate: 100 Hz |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Description: SwissFEL injector / Filter size: 20 µm / Flow rate: 4.2 µL/min / Injector diameter: 75 µm / Injector temperature: 298 K |
Serial crystallography data reduction | Frames indexed: 80479 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7YC7 Resolution: 2.2→16.74 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.81 / 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: 2.2→16.74 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: -22.1111 Å / Origin y: -0.7956 Å / Origin z: -14.7472 Å
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Refinement TLS group | Selection details: all |