[English] 日本語
![](img/lk-miru.gif)
- PDB-5cl8: Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5cl8 | ||||||
---|---|---|---|---|---|---|---|
Title | Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasic site and a free nucleobase (100% product at 144 hours) | ||||||
![]() |
| ||||||
![]() | HYDROLASE/DNA / DNA glycosylase / HEAT-like repeat / protein-DNA complex / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mullins, E.A. / Eichman, B.F. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Authors: Mullins, E.A. / Shi, R. / Parsons, Z.D. / Yuen, P.K. / David, S.S. / Igarashi, Y. / Eichman, B.F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 196.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 154.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5cl3C ![]() 5cl4C ![]() 5cl5C ![]() 5cl6C ![]() 5cl7C ![]() 5cl9C ![]() 5claC ![]() 5clbC ![]() 5clcC ![]() 5cldC ![]() 5cleC ![]() 3bvsS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28578.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: R8GWR7, UniProt: Q816E8*PLUS, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
---|---|
#2: DNA chain | Mass: 3515.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 3694.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-54K / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.99 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 15% w/v PEG4000, 42 mM sodium acetate, pH 4.6, 85 mM ammonium acetate, 5% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 25, 2014 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→50 Å / Num. obs: 64201 / % possible obs: 99.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 14.62 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.38→1.4 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 5.091 / % possible all: 96.1 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3BVS Resolution: 1.38→35.12 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.27 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→35.12 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|