[English] 日本語
Yorodumi- PDB-2end: CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2end | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
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 / 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 | Enterobacteria phage T4 (virus) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.45 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. #1: 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, T. / Katayanagi, K. / Ariyoshi, M. / Doi, T. / Ikehara, M. / Inaoka, T. / Ohtsuka, E. #2: 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. #3: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2end.cif.gz | 43.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2end.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 2end.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2end_validation.pdf.gz | 365.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2end_full_validation.pdf.gz | 370.8 KB | Display | |
Data in XML | 2end_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 2end_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/2end ftp://data.pdbj.org/pub/pdb/validation_reports/en/2end | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16104.574 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 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.37 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 4.5 / Method: vapor diffusion / Details: Morikawa, K., (1988) J. Mol. Biol., 202, 683. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 1.45 Å / % possible obs: 80.2 % / Rmerge(I) obs: 0.048 |
---|
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.45→6 Å / σ(F): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |