[English] 日本語
![](img/lk-miru.gif)
- PDB-5lw6: Crystal structure of a Se-Met substituted Dictyostelium discoideu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5lw6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a Se-Met substituted Dictyostelium discoideum ADP-ribose binding macrodomain (residues 342-563) of DDB_G0293866 | ||||||
![]() | DDB_G0293866 | ||||||
![]() | ADP-RIBOSE BINDING PROTEIN / Macrodomain | ||||||
Function / homology | ![]() response to cisplatin / : / poly-ADP-D-ribose binding / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / double-strand break repair / site of double-strand break / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leys, D. / Barkauskaite, E. / Pinero, B.B. / Ahel, I. | ||||||
![]() | ![]() Title: The role of ADP-ribosylation in regulating DNA interstrand crosslink repair. Authors: Gunn, A.R. / Banos-Pinero, B. / Paschke, P. / Sanchez-Pulido, L. / Ariza, A. / Day, J. / Emrich, M. / Leys, D. / Ponting, C.P. / Ahel, I. / Lakin, N.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 58.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 425.9 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 29474.408 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.99 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: Crystallization trials were performed with proteins at 25 mg/ml in buffer containing 150 mM NaCl, 1 mM DTT and 25 mM Tris-HCl (pH 7.5), at 20 C with commercial screens using the sitting-drop ...Details: Crystallization trials were performed with proteins at 25 mg/ml in buffer containing 150 mM NaCl, 1 mM DTT and 25 mM Tris-HCl (pH 7.5), at 20 C with commercial screens using the sitting-drop vapour-diffusion method. Crystallization drops were set up with the aid of a Mosquito Crystal robot (TTP Labtech) using 200 nl of protein solution plus 200 nl of reservoir solution in MRC two-well crystallization microplates (Swissci) equilibrated against 75 microl of reservoir solution. Co-crystallisation trials were set up by adding 2 mM ADPr to the protein for at least 1 hour prior to setting up crystallisation drops. Crystals of the macrodomain proteins grew in 0.2 M Lithium sulphate, 0.1 M phosphate/citrate and 20% (w/v) PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25.19 Å / Num. obs: 22050 / % possible obs: 99.9 % / Redundancy: 25.8 % / Rsym value: 0.078 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 25.4 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.943 / % possible all: 100 |
-
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.915 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→25.19 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|