[English] 日本語
![](img/lk-miru.gif)
- PDB-5cuz: Crystal structure of SeMet-substituted N-terminal truncated human... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5cuz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SeMet-substituted N-terminal truncated human B12-chaperone CblD (108-296) | ||||||
![]() | Methylmalonic aciduria and homocystinuria type D protein, mitochondrial | ||||||
![]() | CHAPERONE / Vitamin B12 / Nitro-FMN-reductase | ||||||
Function / homology | Methylmalonic aciduria and homocystinuria type D protein / Methylmalonic aciduria and homocystinuria type D protein / Defective MMADHC causes MMAHCD / cobalamin metabolic process / Cobalamin (Cbl) metabolism / mitochondrion / cytosol / cytoplasm / Cobalamin trafficking protein CblD![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamada, K. / Gherasim, C. / Banerjee, R. / Koutmos, M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure of Human B12 Trafficking Protein CblD Reveals Molecular Mimicry and Identifies a New Subfamily of Nitro-FMN Reductases. Authors: Yamada, K. / Gherasim, C. / Banerjee, R. / Koutmos, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 66.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 22074.982 Da / Num. of mol.: 1 / Fragment: UNP residues 108-296 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: 1.8 Å3/Da / Density % sol: 32.2 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 % PEG3350, 0.1M Tris-HCl, pH 7.5, 0.185 M MgCl2, 0.12 M NaF |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2013 Details: K-B pair of biomorph mirrors for vertical and horizontal focusing |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979475 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→50 Å / Num. obs: 6667 / % possible obs: 94.1 % / Redundancy: 7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.31→2.39 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.5 / % possible all: 70.4 |
-
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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.151 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.31→48.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|