+Open data
-Basic information
Entry | Database: PDB / ID: 1qnf | ||||||
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Title | STRUCTURE OF PHOTOLYASE | ||||||
Components | PHOTOLYASE | ||||||
Keywords | DNA REPAIR / ELECTRON TRANSFER / EXCITATION ENERGY TRANSFER / LYASE (CARBON-CARBON) | ||||||
Function / homology | Function and homology information 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 | Synechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | ||||||
Authors | Miki, K. / Kitadokoro, K. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 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: Journal: J.Mol.Biol. / Year: 1993 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qnf.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qnf.ent.gz | 90.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/1qnf ftp://data.pdbj.org/pub/pdb/validation_reports/qn/1qnf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Synechococcus elongatus (bacteria) / Strain: PCC 6301 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 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: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→6 Å / σ(F): 1
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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: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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