[English] 日本語
![](img/lk-miru.gif)
- PDB-2i2l: X-ray Crystal Structure of Protein yopX from Bacillus subtilis. N... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2i2l | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray Crystal Structure of Protein yopX from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR411. | ||||||
![]() | YopX protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / SR411 / yopX / O34401 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | ![]() Complement Module; domain 1 - #50 / YopX protein / YopX protein / Complement Module; domain 1 / SH3 type barrels. - #100 / SH3 type barrels. / Ribbon / Roll / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vorobiev, S.M. / Zhou, W. / Seetharaman, J. / Forouhar, F. / Kuzin, A.A. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. ...Vorobiev, S.M. / Zhou, W. / Seetharaman, J. / Forouhar, F. / Kuzin, A.A. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Acton, T. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of the hypothetical protein yopX from Bacillus subtilis Authors: Vorobiev, S.M. / Zhou, W. / Seetharaman, J. / Forouhar, F. / Kuzin, A.A. / Ho, C.K. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Acton, T. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 86.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 70.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 466.2 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 16420.863 Da / Num. of mol.: 3 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: 2.54 Å3/Da / Density % sol: 51.51 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 4000, 0.2M Sodium acetate, 0.2M Sodium thiocyanate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 8, 2006 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.8→30 Å / Num. all: 23997 / Num. obs: 23973 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.101 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.7 / % possible all: 99.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.3194 Å2 / ksol: 0.255885 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→28.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|