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Open data
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Basic information
Entry | Database: PDB / ID: 4z4k | ||||||
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Title | Crystal structure of GFP-TAX1BP1 UBZ1+2 domain fusion protein | ||||||
![]() | Green fluorescent protein,Tax1-binding protein 1 | ||||||
![]() | Flurorescent Protein / Metal Binding Protein / GFP / TAX1BP1 / UBZ / Zinc-finger | ||||||
Function / homology | ![]() protein localization to phagocytic vesicle / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / negative regulation of NF-kappaB transcription factor activity / autophagosome / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / kinase binding / autophagy ...protein localization to phagocytic vesicle / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / negative regulation of NF-kappaB transcription factor activity / autophagosome / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / kinase binding / autophagy / serine-type endopeptidase inhibitor activity / protein-macromolecule adaptor activity / cytoplasmic vesicle / innate immune response / negative regulation of apoptotic process / apoptotic process / mitochondrion / extracellular space / extracellular exosome / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rohaim, A. / Kawasaki, M. / Wakatsuki, S. | ||||||
![]() | ![]() Title: A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1. Authors: Suzuki, N. / Rohaim, A. / Kato, R. / Dikic, I. / Wakatsuki, S. / Kawasaki, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 240.9 KB | Display | ![]() |
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PDB format | ![]() | 193.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3vhsC ![]() 3vhtC ![]() 3wupC ![]() 4z4mC ![]() 1emaS C: citing same article ( S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 33251.355 Da / Num. of mol.: 2 / Fragment: UBZ1 and UBZ2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: GFP, TAX1BP1, T6BP, PRO0105 / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% w/v PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 14819 / % possible obs: 99.64 % / Redundancy: 6.6 % / Net I/σ(I): 4.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EMA Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.869 / SU B: 37.403 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R Free: 0.449 / 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: 44.733 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→50 Å
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Refine LS restraints |
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