[English] 日本語
![](img/lk-miru.gif)
- PDB-8h1e: Aquifex aeolicus MutL endonuclease domain complexed with manganes... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8h1e | ||||||
---|---|---|---|---|---|---|---|
Title | Aquifex aeolicus MutL endonuclease domain complexed with manganese ions | ||||||
![]() | DNA mismatch repair protein MutL | ||||||
![]() | DNA BINDING PROTEIN / endonuclease | ||||||
Function / homology | ![]() mismatch repair complex / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fukui, K. / Yano, T. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Catalytic mechanism of the zinc-dependent MutL endonuclease reaction. Authors: Fukui, K. / Yamamoto, T. / Murakawa, T. / Baba, S. / Kumasaka, T. / Yano, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 70 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 43.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 4.1 MB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h1fC ![]() 8h1gC ![]() 5b42S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12352.259 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-PEG / | ||||
#3: Chemical | ChemComp-MN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.95 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 200 mM sodium acetate, 50 mM MnCl2, and 30 % (v/v) polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→32.8 Å / Num. obs: 33594 / % possible obs: 99.7 % / Redundancy: 14.4 % / Biso Wilson estimate: 17.91 Å2 / CC1/2: 0.95 / Net I/σ(I): 60 |
Reflection shell | Resolution: 1.22→1.26 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3304 / CC1/2: 0.59 / Rpim(I) all: 0.53 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5B42 Resolution: 1.22→32.8 Å / SU ML: 0.149 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.8343 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→32.8 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|