[English] 日本語
Yorodumi- PDB-1udg: THE STRUCTURAL BASIS OF SPECIFIC BASE EXCISION REPAIR BY URACIL-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1udg | ||||||
---|---|---|---|---|---|---|---|
Title | THE STRUCTURAL BASIS OF SPECIFIC BASE EXCISION REPAIR BY URACIL-DNA GLYCOSYLASE | ||||||
Components | URACIL-DNA GLYCOSYLASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / host cell nucleus Similarity search - Function | ||||||
Biological species | Herpes simplex virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.75 Å | ||||||
Authors | Pearl, L.H. / Savva, R. | ||||||
Citation | Journal: Nature / Year: 1995 Title: The structural basis of specific base-excision repair by uracil-DNA glycosylase. Authors: Savva, R. / McAuley-Hecht, K. / Brown, T. / Pearl, L. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization and Preliminary X-Ray Analysis of the Uracil-DNA Glycosylase DNA Repair Enzyme from Herpes Simplex Virus Type 1 Authors: Savva, R. / Pearl, L.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1udg.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1udg.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 1udg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/1udg ftp://data.pdbj.org/pub/pdb/validation_reports/ud/1udg | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: CIS PROLINE - PRO 63 |
-Components
#1: Protein | Mass: 27366.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: ENCODED BY THE UL2 ORF OF HERPES SIMPLEX VIRUS TYPE 1 Source: (natural) Herpes simplex virus (type 1 / strain 17) / Genus: Simplexvirus / Species: Human herpesvirus 1Herpesviridae / Strain: 17 / References: UniProt: P10186, uridine nucleosidase | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.05 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6.8 / Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Wavelength: 0.88 Å |
---|---|
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88 Å / Relative weight: 1 |
Reflection | Num. obs: 22566 / % possible obs: 95.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.055 |
Reflection | *PLUS Highest resolution: 1.75 Å / Rmerge(I) obs: 0.055 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.75→8 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |