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Yorodumi- PDB-7ayv: X-ray crystallographic structure of (6-4)photolyase from Drosophi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ayv | ||||||
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Title | X-ray crystallographic structure of (6-4)photolyase from Drosophila melanogaster at cryogenic temperature | ||||||
Components | RE11660p | ||||||
Keywords | LYASE / Flavoprotein / (6-4)photolyase | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Cellini, A. / Wahlgren, W.Y. / Henry, L. / Westenhoff, S. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature. Authors: Cellini, A. / Yuan Wahlgren, W. / Henry, L. / Pandey, S. / Ghosh, S. / Castillon, L. / Claesson, E. / Takala, H. / Kubel, J. / Nimmrich, A. / Kuznetsova, V. / Nango, E. / Iwata, S. / Owada, ...Authors: Cellini, A. / Yuan Wahlgren, W. / Henry, L. / Pandey, S. / Ghosh, S. / Castillon, L. / Claesson, E. / Takala, H. / Kubel, J. / Nimmrich, A. / Kuznetsova, V. / Nango, E. / Iwata, S. / Owada, S. / Stojkovic, E.A. / Schmidt, M. / Ihalainen, J.A. / Westenhoff, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ayv.cif.gz | 209.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ayv.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ayv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ayv_validation.pdf.gz | 403.4 KB | Display | wwPDB validaton report |
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Full document | 7ayv_full_validation.pdf.gz | 405.6 KB | Display | |
Data in XML | 7ayv_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 7ayv_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/7ayv ftp://data.pdbj.org/pub/pdb/validation_reports/ay/7ayv | HTTPS FTP |
-Related structure data
Related structure data | 7aztC 3cvyS S: Starting model for refinement C: citing same article (ref.) |
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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: 58313.043 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 K-12 (bacteria) / References: UniProt: Q8SXK5 | ||||
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#2: Chemical | ChemComp-GOL / | ||||
#3: Chemical | ChemComp-FAD / | ||||
#4: Chemical | ChemComp-SO4 / #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: 2.6 Å3/Da / Density % sol: 52.75 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Lithium sulphate, 0.1 M Bis-Tris(pH=6.5), 25%PEG3350, 4% polypropylene glycol p 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→29.42 Å / Num. obs: 58656 / % possible obs: 99.2 % / Redundancy: 12.7 % / Biso Wilson estimate: 25.32 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.79→1.854 Å / Num. unique obs: 3836 / CC1/2: 0.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3cvy Resolution: 1.79→29.42 Å / SU ML: 0.2196 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.858 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: 26.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→29.42 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 |
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