[English] 日本語
![](img/lk-miru.gif)
- PDB-3vgp: Crystal structure of the C-terminal globular domain of oligosacch... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3vgp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the C-terminal globular domain of oligosaccharyltransferase (AF_0329) from Archaeoglobus fulgidus | ||||||
![]() | Transmembrane oligosaccharyl transferase, putative | ||||||
![]() | TRANSFERASE / glycosyltransferase / cell membrane | ||||||
Function / homology | ![]() oligosaccharyl transferase activity / dolichyl-phosphooligosaccharide-protein glycotransferase / protein glycosylation / membrane => GO:0016020 / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matsumoto, S. / Igura, M. / Nyirenda, J. / Yuzawa, S. / Noda, N.N. / Inagaki, F. / Kohda, D. | ||||||
![]() | ![]() Title: Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase from Archaeoglobus fulgidus at 1.75 A Resolution Authors: Matsumoto, S. / Igura, M. / Nyirenda, J. / Matsumoto, M. / Yuzawa, S. / Noda, N.N. / Inagaki, F. / Kohda, D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 44.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 34.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 424.7 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 19292.887 Da / Num. of mol.: 1 / Fragment: C-terminal globular domain / Mutation: C482A 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: 2.29 Å3/Da / Density % sol: 46.33 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12.5% PEG 3350, 0.1M bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
---|---|
Detector | Type: BRUKER SMART 6500 / Detector: CCD / Date: Jul 22, 2010 |
Radiation | Monochromator: a double-crystal monochromator and a horizontal focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 19197 / Num. obs: 18986 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 27 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 98.6 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 24.8 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 13 / Num. unique all: 853 / % possible all: 93.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.7233 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→40.54 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|