[English] 日本語
![](img/lk-miru.gif)
- PDB-1n3a: Structural and biochemical exploration of a critical amino acid i... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1n3a | ||||||
---|---|---|---|---|---|---|---|
Title | Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase | ||||||
![]() |
| ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Norman, D.P. / Chung, S.J. / Verdine, G.L. | ||||||
![]() | ![]() Title: Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase Authors: Norman, D.P. / Chung, S.J. / Verdine, G.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 95.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1n39C ![]() 1n3cC ![]() 1fn7S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 4635.010 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: DNA chain | Mass: 4396.838 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 35661.348 Da / Num. of mol.: 1 / Mutation: D268Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: O15527, ![]() ![]() |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.36 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: cacodylate, calcium acetate, 16-18% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Details: Bruner, S.D., (2000) Nature, 403, 859. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→30 Å / Num. all: 30819 / Num. obs: 29555 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.2→2.34 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4.7 / % possible all: 92.4 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Num. obs: 29555 / % possible obs: 95.9 % / Num. measured all: 149944 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 92.4 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 1FN7 Resolution: 2.2→29.93 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.7526 Å2 / ksol: 0.349783 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.5 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.35 Å / Luzzati sigma a free: 0.33 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→29.93 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree![]() | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.34 / Rfactor Rwork: 0.33 |