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- PDB-1vas: ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vas | ||||||
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Title | ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITION | ||||||
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![]() | HYDROLASE/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() deoxyribodipyrimidine endonucleosidase / pyrimidine dimer DNA N-glycosylase activity / deoxyribodipyrimidine endonucleosidase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / endonuclease activity / DNA repair Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Vassylyev, D.G. / Kashiwagi, T. / Mikami, Y. / Ariyoshi, M. / Iwai, S. / Ohtsuka, E. / Morikawa, K. | ||||||
![]() | ![]() Title: Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. Authors: Vassylyev, D.G. / Kashiwagi, T. / Mikami, Y. / Ariyoshi, M. / Iwai, S. / Ohtsuka, E. / Morikawa, K. #1: ![]() Title: Crystal Structure of a Pyrimidine Dimer-Specific Excision Repair Enzyme from Bacteriophage T4: Refinement at 1.45 Angstroms and X-Ray Analysis of the Three Active Site Mutants Authors: Morikawa, K. / Ariyoshi, M. / Vassylyev, D.G. / Matsumoto, O. / Katayanagi, K. / Ohtsuka, E. #3: ![]() Title: Role of the Basic Amino Acid Cluster and Glu-23 in Pyrimidine Dimer Glycosylase Activity of T4 Endonuclease V Authors: Doi, T. / Recktenwald, A. / Karaki, Y. / Kikuchi, M. / Morikawa, K. / Ikehara, M. / Inaoka, T. / Hori, N. / Ohtsuka, E. #4: ![]() Title: X-Ray Structure of T4 Endonuclease V: An Excision Repair Enzyme Specific for a Pyrimidine Dimer Authors: Morikawa, K. / Matsumoto, O. / Tsujimoto, M. / Katayanagi, K. / Ariyoshi, M. / Doi, T. / Ikehara, M. / Inaoka, T. / Ohtsuka, E. #5: ![]() Title: Preliminary Crystallographic Study of Pyrimidine Dimer-Specific Excision Repair Enzyme from Bacteriophage T4 Authors: Morikawa, K. / Tsujimoto, M. / Ikehara, M. / Inaoka, T. / Ohtsuka, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60 KB | Display | ![]() |
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PDB format | ![]() | 40.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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: DNA chain | Mass: 3958.571 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3985.613 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 15972.392 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.21 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE DIP100 / Detector: IMAGE PLATE / Date: Jun 3, 1994 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 5662 / % possible obs: 72 % / Observed criterion σ(F): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.062 |
Reflection | *PLUS Highest resolution: 2.75 Å / Lowest resolution: 50 Å / % possible obs: 72 % / Observed criterion σ(F): 2 / Num. measured all: 24907 |
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Processing
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Refinement | Resolution: 2.75→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 7.8 Å2 | ||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→10 Å
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Software | *PLUS Name: ![]() | ||||||||||||||||
Refinement | *PLUS Highest resolution: 2.75 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.24 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS Biso mean: 7.8 Å2 | ||||||||||||||||
Refine LS restraints | *PLUS
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