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Yorodumi- PDB-1enk: CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1enk | ||||||
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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 | ||||||
Components | ENDONUCLEASE V | ||||||
Keywords | ENDONUCLEASE | ||||||
Function / homology | Function and homology information deoxyribodipyrimidine endonucleosidase / pyrimidine dimer DNA N-glycosylase activity / deoxyribodipyrimidine endonucleosidase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / endonuclease activity / DNA repair Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Vassylyev, D.G. / Ariyoshi, M. / Matsumoto, O. / Katayanagi, K. / Ohtsuka, E. / Morikawa, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants. Authors: Morikawa, K. / Ariyoshi, M. / Vassylyev, D.G. / Matsumoto, O. / Katayanagi, K. / Ohtsuka, E. #2: Journal: Science / Year: 1992 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. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: Role of the Basic Amino Acid Cluster and Glu-23 in Pyrimidine Dimeer 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: Journal: J.Mol.Biol. / Year: 1988 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1enk.cif.gz | 41.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1enk.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 1enk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/1enk ftp://data.pdbj.org/pub/pdb/validation_reports/en/1enk | HTTPS FTP |
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-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: 16090.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / References: UniProt: P04418, EC: 3.1.25.1 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.29 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion / Details: Morikawa, K., (1988) J. Mol. Biol., 202, 683. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2 Å / % possible obs: 93 % / Rmerge(I) obs: 0.084 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→10 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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