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- PDB-8c69: Light SFX structure of D.m(6-4)photolyase at 100 microsecond time... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c69 | ||||||
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Title | Light SFX structure of D.m(6-4)photolyase at 100 microsecond time delay | ||||||
![]() | Cryptochrome-1![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cellini, A. / Kumar, M. / Nimmrich, A. / Mutisya, J. / Furrer, A. / Beale, E.V. / Carrillo, M. / Malla, T.N. / Maj, P. / Dworkowskic, F. ...Cellini, A. / Kumar, M. / Nimmrich, A. / Mutisya, J. / Furrer, A. / Beale, E.V. / Carrillo, M. / Malla, T.N. / Maj, P. / Dworkowskic, F. / Cirelli, C. / Ozerovi, D. / Bacellar, C. / Strandfuss, J. / Weinert, T. / Ihalainen, J.A. / Yuan Wahlgren, W. / Westenhoff, S. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography. Authors: Cellini, A. / Shankar, M.K. / Nimmrich, A. / Hunt, L.A. / Monrroy, L. / Mutisya, J. / Furrer, A. / Beale, E.V. / Carrillo, M. / Malla, T.N. / Maj, P. / Vrhovac, L. / Dworkowski, F. / ...Authors: Cellini, A. / Shankar, M.K. / Nimmrich, A. / Hunt, L.A. / Monrroy, L. / Mutisya, J. / Furrer, A. / Beale, E.V. / Carrillo, M. / Malla, T.N. / Maj, P. / Vrhovac, L. / Dworkowski, F. / Cirelli, C. / Johnson, P.J.M. / Ozerov, D. / Stojkovic, E.A. / Hammarstrom, L. / Bacellar, C. / Standfuss, J. / Maj, M. / Schmidt, M. / Weinert, T. / Ihalainen, J.A. / Wahlgren, W.Y. / Westenhoff, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 247.2 KB | Display | ![]() |
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PDB format | ![]() | 154.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8c1uC ![]() 8c6aC ![]() 8c6bC ![]() 8c6cC ![]() 8c6fC ![]() 8c6hC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 58079.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FAD / ![]() |
#3: Chemical | ChemComp-GOL / ![]() |
#4: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.28 % |
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Crystal grow![]() | Temperature: 277.15 K / Method: batch mode / pH: 6.5 Details: 100 mM bis-tris pH=6.5, 200 mM lithium sulphate monohydrate, 22 % PEG 3350, 0.5 % Ethyl acetate. |
-Data collection
Diffraction | Mean temperature: 293.15 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Sep 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→15.72 Å / Num. obs: 44135 / % possible obs: 99.99 % / Redundancy: 88.9 % / Biso Wilson estimate: 4.81 Å2 / R split: 0.11 / Net I/σ(I): 8.76 |
Reflection shell | Resolution: 1.9→1.91 Å / Num. unique obs: 1766 / R split: 0.41 |
Serial crystallography sample delivery | Method: injection |
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Processing
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Refinement | Method to determine structure![]() ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→15.72 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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