[English] 日本語
![](img/lk-miru.gif)
- PDB-2b0a: Crystal structure of protein MJ0783 from Methanococcus jannaschii -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2b0a | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of protein MJ0783 from Methanococcus jannaschii | ||||||
![]() | Hypothetical protein MJ0783![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patskovsky, Y. / Ramagopal, U. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Crystal Structure of Hypothetical Protein Mj0783 from Methanococcus Jannaschii Authors: Patskovsky, Y. / Ramagopal, U. / Almo, S.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 52.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 38.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
| ||||||||||||
Details | The second part of the biological assembly is generated by the two fold axis: -x+1, y, -z+1 |
-
Components
#1: Protein | ![]() Mass: 21122.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: MJ0783 / Plasmid: pET / Species (production host): Escherichia coli / Production host: ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 45.8 % |
---|---|
Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG 550, 100 mM Tris-HCl, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 87 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTAM Q315 / Detector: CCD / Date: Sep 2, 2005 / Details: MIRRORS | |||||||||
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.45→50 Å / Num. all: 34059 / Num. obs: 34059 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Rsym value: 0.063 / Net I/σ(I): 16.1 | |||||||||
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.35 / % possible all: 96.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: NONE Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.359 / SU ML: 0.053 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.091 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.448→1.486 Å / Total num. of bins used: 20
|