+
Open data
-
Basic information
Entry | Database: PDB / ID: 1c8n | ||||||
---|---|---|---|---|---|---|---|
Title | TOBACCO NECROSIS VIRUS | ||||||
![]() | COAT PROTEIN | ||||||
![]() | VIRUS / Icosahedral virus | ||||||
Function / homology | ![]() T=3 icosahedral viral capsid / structural molecule activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oda, Y. / Fukuyama, K. | ||||||
![]() | ![]() Title: Crystal structure of tobacco necrosis virus at 2.25 A resolution. Authors: Oda, Y. / Saeki, K. / Takahashi, Y. / Maeda, T. / Naitow, H. / Tsukihara, T. / Fukuyama, K. #1: ![]() Title: Crystal Structural Analysis of Tobacco Necrosis Virus at 5 Angstrom Resolution Authors: Bando, M. / Morimoto, Y. / Sato, T. / Tsukihara, T. / Yokota, Y. / Fukuyama, K. / Matsubara, H. #2: ![]() Title: Symmetry and Subunit Arrangement of Tobacco Necrosis Virus (TNV) Authors: Tsukihara, T. / Yokota, Y. / Koyama, T. / Fukuyama, K. / Matsubara, H. #3: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Studies of Tobacco Necrosis Virus Authors: Fukuyama, K. / Hirota, S. / Tsukihara, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 130.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 101 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444.8 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1tnvS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 60||||||||||||||||||
2 |
| ||||||||||||||||||
3 | ![]()
| x 5||||||||||||||||||
4 | ![]()
| x 6||||||||||||||||||
5 | ![]()
| ||||||||||||||||||
6 | ![]()
| x 5||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
#1: Protein | Mass: 29985.188 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: THIS STRAIN IS CLOSE TO STRAIN A. / Source: (natural) ![]() #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal grow | pH: 6 / Details: pH 6.0 |
---|---|
Crystal grow | *PLUS Method: microdialysis |
Components of the solutions | *PLUS Conc.: 0.4 M / Common name: sodium phosphate |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 298768 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.2 / % possible all: 95.6 |
Reflection | *PLUS % possible obs: 99 % / Num. measured all: 842131 |
Reflection shell | *PLUS % possible obs: 95.6 % |
-
Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1TNV Resolution: 2.25→8 Å / Isotropic thermal model: RESTRAINED / σ(F): 2
| ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→8 Å
| ||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS |