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Open data
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Basic information
Entry | Database: PDB / ID: 1qnf | ||||||
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Title | STRUCTURE OF PHOTOLYASE | ||||||
![]() | PHOTOLYASE | ||||||
![]() | DNA REPAIR / ELECTRON TRANSFER / EXCITATION ENERGY TRANSFER / LYASE (CARBON-CARBON) | ||||||
Function / homology | ![]() deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / entrainment of circadian clock by photoperiod / FAD binding / circadian regulation of gene expression / DNA repair / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miki, K. / Kitadokoro, K. | ||||||
![]() | ![]() Title: Crystal structure of DNA photolyase from Anacystis nidulans Authors: Tamada, T. / Kitadokoro, K. / Higuchi, Y. / Inaka, K. / Yasui, A. / de Ruiter, P.E. / Eker, A.P. / Miki, K. #1: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Studies of Photolyase (Photoreactivating Enzyme) from the Cyanobacterium Anacystis Nidulans Authors: Miki, K. / Tamada, T. / Nishida, H. / Inaka, K. / Yasui, A. / De Ruiter, P.E. / Eker, A.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.9 KB | Display | ![]() |
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PDB format | ![]() | 90.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 54531.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: PHOTOREACTIVATING ENZYME / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P05327, deoxyribodipyrimidine photo-lyase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-HDF / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 20%(W/V) AMMONIUM SULFATE, 10MM POTASSIUM PHOSPHATE (PH7.0) | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: IMAGE PLATE |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 246336 / % possible obs: 83.3 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.076 |
Reflection shell | Highest resolution: 1.8 Å |
Reflection | *PLUS Num. obs: 44414 / Num. measured all: 246336 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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