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Yorodumi- PDB-7azt: X-ray crystallographic structure of (6-4)photolyase from Drosophi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7azt | ||||||
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Title | X-ray crystallographic structure of (6-4)photolyase from Drosophila melanogaster at room 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Cellini, A. / Wahlgren, W.Y. / Henry, L. / Westenhoff, S. / Pandey, 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 | 7azt.cif.gz | 136 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7azt.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 7azt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7azt_validation.pdf.gz | 383.7 KB | Display | wwPDB validaton report |
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Full document | 7azt_full_validation.pdf.gz | 386.4 KB | Display | |
Data in XML | 7azt_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 7azt_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/7azt ftp://data.pdbj.org/pub/pdb/validation_reports/az/7azt | HTTPS FTP |
-Related structure data
Related structure data | 7ayvSC 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: 58310.973 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-FAD / |
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: 2.81 Å3/Da / Density % sol: 56.2 % |
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Crystal grow | Temperature: 277.15 K / Method: batch mode / pH: 6.5 Details: 0.2 M lithium sulftate, 0.1 M bis-tris (pH=6.5), 25% PEG3350, 4% polypropyle glycol P400 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.7712 Å |
Detector | Type: MPCCD / Detector: CCD / Date: May 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→42.61 Å / Num. obs: 33953 / % possible obs: 100 % / Redundancy: 106 % / Biso Wilson estimate: 90.69 Å2 / CC1/2: 0.97 / Net I/σ(I): 4.93 |
Reflection shell | Resolution: 2.27→2.351 Å / Num. unique obs: 1352 / CC1/2: 0.32 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AYV Resolution: 2.27→42.61 Å / SU ML: 0.3689 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0904 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: 93.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→42.61 Å
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Refine LS restraints |
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LS refinement shell |
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