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Yorodumi- PDB-1own: DATA3:DNA photolyase / received X-rays dose 4.8 exp15 photons/mm2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1own | ||||||
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Title | DATA3:DNA photolyase / received X-rays dose 4.8 exp15 photons/mm2 | ||||||
Components | Deoxyribodipyrimidine photolyase | ||||||
Keywords | LYASE / DNA repair / flavin enzyme / Photoreactivating enzyme | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Komori, H. / Adachi, S. / Miki, K. / Eker, A. / Kort, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: DNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF reconstitution and X-ray-induced FAD reduction. Authors: Kort, R. / Komori, H. / Adachi, S. / Miki, K. / Eker, A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallography & NMR System Authors: Brunger, A.T. / Adams, P.D. / Clore, G.M. / Delano, W.L. / Gros, P. / Grosse-Kunstleve, R. / Jiang, J.-S. / Kuszewski, J. / Nilges, M. / Pannu, N.S. / Read, R.J. / Rice, L.M. / Simonson, T. / Warren, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1own.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1own.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 1own.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1own_validation.pdf.gz | 810.1 KB | Display | wwPDB validaton report |
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Full document | 1own_full_validation.pdf.gz | 818.6 KB | Display | |
Data in XML | 1own_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 1own_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/1own ftp://data.pdbj.org/pub/pdb/validation_reports/ow/1own | HTTPS FTP |
-Related 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: 54531.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 6301 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) References: UniProt: P05327, deoxyribodipyrimidine photo-lyase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-FAD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Ammonium Sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 29, 2002 |
Radiation | Monochromator: fix-exit double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.97 Å / Num. all: 24626 / Num. obs: 24483 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Biso Wilson estimate: 26.3 Å2 / Limit h max: 38 / Limit h min: 0 / Limit k max: 27 / Limit k min: 0 / Limit l max: 57 / Limit l min: 0 / Observed criterion F max: 2977585.95 / Observed criterion F min: 26.9 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 70.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.97 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 40.4677 Å2 / ksol: 0.362455 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.15 Å2 / Biso mean: 29.3 Å2 / Biso min: 9.86 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.97 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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