[English] 日本語
![](img/lk-miru.gif)
- PDB-8iia: Crystal structure of the oligomeric state of the extracellular do... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8iia | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the oligomeric state of the extracellular domain of human myelin protein zero(MPZ/P0) | ||||||||||||||||||
![]() | Myelin protein P0 | ||||||||||||||||||
![]() | CELL ADHESION / membrane adhesion / oligomeric state | ||||||||||||||||||
Function / homology | ![]() cell aggregation / cell-cell adhesion via plasma-membrane adhesion molecules / EGR2 and SOX10-mediated initiation of Schwann cell myelination / myelination / myelin sheath / chemical synaptic transmission / synapse / structural molecule activity / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Sakakura, M. / Tanabe, M. / Mio, K. | ||||||||||||||||||
Funding support | ![]()
| ||||||||||||||||||
![]() | ![]() Title: Structural bases for the Charcot-Marie-Tooth disease induced by single amino acid substitutions of myelin protein zero. Authors: Sakakura, M. / Tanabe, M. / Mori, M. / Takahashi, H. / Mio, K. | ||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 47.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 26.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 441.2 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1neuS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 14066.645 Da / Num. of mol.: 1 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.1 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl, 300 mM magnesium-formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→44.49 Å / Num. obs: 10861 / % possible obs: 100 % / Redundancy: 26.8 % / Biso Wilson estimate: 49.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.028 / Net I/av σ(I): 13.9 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.09→2.14 Å / Redundancy: 27.4 % / Rmerge(I) obs: 3.297 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 815 / CC1/2: 0.815 / Rpim(I) all: 0.634 / % possible all: 99.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1NEU Resolution: 2.09→36.27 Å / SU ML: 0.2521 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.1569 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: 52.75 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→36.27 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|