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- PDB-3a9k: Crystal structure of the mouse TAB3-NZF in complex with Lys63-lin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a9k | ||||||
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Title | Crystal structure of the mouse TAB3-NZF in complex with Lys63-linked di-ubiquitin | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sato, Y. / Yoshikawa, A. / Yamashita, M. / Yamagata, A. / Fukai, S. | ||||||
![]() | ![]() Title: Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3 Authors: Sato, Y. / Yoshikawa, A. / Yamashita, M. / Yamagata, A. / Fukai, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.7 KB | Display | ![]() |
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PDB format | ![]() | 68.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3a9jSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | CHAINS A AND B ARE COVALENTLY BONDED TO FORM A SINGLE MOLECULE. THIS MOLECULE FORM A HETERO DIMERIC COMPLEX WITH CHAIN C. |
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Components
#1: Protein | ![]() Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K63R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 8691.918 Da / Num. of mol.: 1 / Mutation: 77D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 3841.340 Da / Num. of mol.: 1 / Fragment: RanBP2-type, residues 688-716 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.8 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100mM Bis-Tris-HCl (pH 6.5), 21% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 29, 2009 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.4→50 Å / Num. all: 30844 / Num. obs: 30844 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05 / Net I/σ(I): 36.8 |
Reflection shell | Resolution: 1.4→1.42 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.78 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3A9J Resolution: 1.4→25.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.701 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 18.054 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→25.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.437 Å / Total num. of bins used: 20
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