+Open data
-Basic information
Entry | Database: PDB / ID: 1dnp | ||||||
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Title | STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE | ||||||
Components | DNA PHOTOLYASE | ||||||
Keywords | LYASE (CARBON-CARBON) / DNA REPAIR / ELECTRON TRANSFER / EXCITATION ENERGY TRANSFER / LYASE / CARBON-CARBON | ||||||
Function / homology | Function and homology information deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / : / DNA repair / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Park, H.-W. / Sancar, A. / Deisenhofer, J. | ||||||
Citation | Journal: Science / Year: 1995 Title: Crystal structure of DNA photolyase from Escherichia coli. Authors: Park, H.W. / Kim, S.T. / Sancar, A. / Deisenhofer, J. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization and Preliminary Crystallographic Analysis of Escherichia Coli DNA Photolyase Authors: Park, H.W. / Sancar, A. / Deisenhofer, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dnp.cif.gz | 205.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dnp.ent.gz | 164.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/1dnp ftp://data.pdbj.org/pub/pdb/validation_reports/dn/1dnp | 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.025044, -0.324306, -0.945621), Vector: |
-Components
#1: Protein | Mass: 53601.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PHOTOREACTIVATING ENZYME / Source: (natural) Escherichia coli (E. coli) References: UniProt: P00914, deoxyribodipyrimidine photo-lyase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 / Method: vapor diffusionDetails: seeding. refer to Park, H.W., (1993) J.Mol.Biol., 231, 1122. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
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Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 1, 1991 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.3 Å / Num. obs: 33086 / % possible obs: 78.3 % / Observed criterion σ(I): 2 / Redundancy: 2.45 % / Rmerge(I) obs: 0.043 |
Reflection | *PLUS Num. measured all: 76311 |
-Processing
Software |
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Refinement | Resolution: 2.3→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 17.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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