+Open data
-Basic information
Entry | Database: PDB / ID: 6l9w | |||||||||
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Title | Crystal structure of mouse TIFA (T9E/C36S mutant) | |||||||||
Components | TRAF-interacting protein with FHA domain-containing protein A | |||||||||
Keywords | SIGNALING PROTEIN / FHA domain | |||||||||
Function / homology | Function and homology information Alpha-protein kinase 1 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / cytoplasmic pattern recognition receptor signaling pathway / 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 | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Nakamura, T. / Yamagata, Y. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Sci Rep / Year: 2020 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: Journal: To Be Published Title: Crystallization and preliminary X-ray analysis of mouse TIFA Authors: Nakamura, T. / Inoue, J. / Yamagata, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l9w.cif.gz | 182 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l9w.ent.gz | 144.3 KB | Display | PDB format |
PDBx/mmJSON format | 6l9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l9w_validation.pdf.gz | 480.8 KB | Display | wwPDB validaton report |
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Full document | 6l9w_full_validation.pdf.gz | 487.7 KB | Display | |
Data in XML | 6l9w_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 6l9w_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/6l9w ftp://data.pdbj.org/pub/pdb/validation_reports/l9/6l9w | HTTPS FTP |
-Related structure data
Related structure data | 6l9uSC 6l9vC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-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.) Mus musculus (house mouse) / Gene: Tifa, T2bp / Production host: Escherichia coli (E. coli) / References: UniProt: Q793I8 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.1 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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