+Open data
-Basic information
Entry | Database: PDB / ID: 8c1u | ||||||
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Title | SFX structure of D.m(6-4)photolyase | ||||||
Components | Cryptochrome-1 | ||||||
Keywords | FLAVOPROTEIN / photolyase / SFX / FAD | ||||||
Function / homology | Function and homology information deoxyribodipyrimidine photo-lyase activity / entrainment of circadian clock by photoperiod / FAD binding / circadian regulation of gene expression / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | 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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Citation | Journal: Nat.Chem. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c1u.cif.gz | 149.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c1u.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 8c1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/8c1u ftp://data.pdbj.org/pub/pdb/validation_reports/c1/8c1u | HTTPS FTP |
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-Related structure data
Related structure data | 8c69C 8c6aC 8c6bC 8c6cC 8c6fC 8c6hC 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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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.) Drosophila melanogaster (fruit fly) / Gene: phr6-4, CG2488 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8SXK5 |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1 Å |
Detector | Type: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Sep 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→16.93 Å / Num. obs: 61453 / % possible obs: 99.99 % / Redundancy: 352.35 % / Biso Wilson estimate: 24.85 Å2 / R split: 0.12 / Net I/σ(I): 6.89 |
Reflection shell | Resolution: 1.7→1.71 Å / Num. unique obs: 2414 / R split: 0.95 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→16.93 Å / SU ML: 0.2129 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2982 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: 33.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→16.93 Å
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Refine LS restraints |
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LS refinement shell |
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