+
Open data
-
Basic information
Entry | Database: PDB / ID: 6l9w | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of mouse TIFA (T9E/C36S mutant) | |||||||||
![]() | TRAF-interacting protein with FHA domain-containing protein A | |||||||||
![]() | SIGNALING PROTEIN / FHA domain | |||||||||
Function / homology | ![]() Alpha-protein kinase 1 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / cytoplasmic pattern recognition receptor signaling pathway / canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / protein homooligomerization / positive regulation of canonical NF-kappaB signal transduction / innate immune response / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nakamura, T. / Yamagata, Y. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural analysis of TIFA: Insight into TIFA-dependent signal transduction in innate immunity. Authors: Nakamura, T. / Hashikawa, C. / Okabe, K. / Yokote, Y. / Chirifu, M. / Toma-Fukai, S. / Nakamura, N. / Matsuo, M. / Kamikariya, M. / Okamoto, Y. / Gohda, J. / Akiyama, T. / Semba, K. / ...Authors: Nakamura, T. / Hashikawa, C. / Okabe, K. / Yokote, Y. / Chirifu, M. / Toma-Fukai, S. / Nakamura, N. / Matsuo, M. / Kamikariya, M. / Okamoto, Y. / Gohda, J. / Akiyama, T. / Semba, K. / Ikemizu, S. / Otsuka, M. / Inoue, J.I. / Yamagata, Y. #1: ![]() Title: Crystallization and preliminary X-ray analysis of mouse TIFA Authors: Nakamura, T. / Inoue, J. / Yamagata, Y. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 182 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 144.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 487.7 KB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 38.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6l9uSC ![]() 6l9vC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 22663.414 Da / Num. of mol.: 6 / Mutation: T9E,C36S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.1 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: MES pH 6.4, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jan 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→37.29 Å / Num. obs: 28175 / % possible obs: 95.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.294 / Num. unique obs: 2170 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6L9U Resolution: 2.9→37.29 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.79
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.62 Å2 / Biso mean: 61.7854 Å2 / Biso min: 17.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→37.29 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|