[English] 日本語
![](img/lk-miru.gif)
- PDB-4oky: Crystal structure of PvuRts1I, a 5-hydroxymethylcytosine DNA rest... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4oky | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease | ||||||
![]() | Restriction endonuclease PvuRts1 I | ||||||
![]() | DNA BINDING PROTEIN / SRA-like domain / restriction endonuclease | ||||||
Function / homology | SET and RING associated domain / : / SET and RING associated domain / Restriction endonuclease PvuRts1 I-like, N-terminal / endonuclease activity / Restriction endonuclease PvuRts1 I![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, C.L. / Shao, C. / Zang, J.Y. | ||||||
![]() | ![]() Title: Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease Authors: Shao, C. / Wang, C. / Zang, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 63.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 50.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 442.3 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34524.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.19 Å3/Da / Density % sol: 70.67 % |
---|---|
Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 1.128M NaH2PO4, 0.752M K2HPO4, 0.1M CAPS pH 10.5, 0.19M Li2SO4, 6%(v/v) glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 286K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2013 |
Radiation | Monochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→56.71 Å / Num. all: 13568 / Num. obs: 13311 / % possible obs: 98.1 % / Observed criterion σ(F): 12.9 / Observed criterion σ(I): 12.9 / Redundancy: 10.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.258 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→56.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|