+Open data
-Basic information
Entry | Database: PDB / ID: 3dkb | ||||||
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Title | Crystal Structure of A20, 2.5 angstrom | ||||||
Components | Tumor necrosis factor, alpha-induced protein 3 | ||||||
Keywords | HYDROLASE / OTU domain / DUB domain / Apoptosis / Cytoplasm / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Protease / Thiol protease / Ubl conjugation pathway / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information regulation of vascular wound healing / negative regulation of toll-like receptor 5 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / establishment of protein localization to vacuole / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / negative regulation of B cell activation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway ...regulation of vascular wound healing / negative regulation of toll-like receptor 5 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / establishment of protein localization to vacuole / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / negative regulation of B cell activation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / negative regulation of toll-like receptor 2 signaling pathway / protein K11-linked deubiquitination / negative regulation of chronic inflammatory response / : / negative regulation of toll-like receptor 4 signaling pathway / regulation of germinal center formation / B-1 B cell homeostasis / protein K48-linked deubiquitination / regulation of defense response to virus by host / regulation of tumor necrosis factor-mediated signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / protein K63-linked deubiquitination / positive regulation of hepatocyte proliferation / negative regulation of bone resorption / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of interleukin-2 production / negative regulation of interleukin-1 beta production / K63-linked deubiquitinase activity / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of interleukin-6 production / response to muramyl dipeptide / positive regulation of Wnt signaling pathway / negative regulation of tumor necrosis factor production / protein K48-linked ubiquitination / negative regulation of endothelial cell apoptotic process / negative regulation of canonical NF-kappaB signal transduction / cytoskeleton organization / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of protein ubiquitination / negative regulation of innate immune response / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Negative regulators of DDX58/IFIH1 signaling / negative regulation of smooth muscle cell proliferation / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / response to molecule of bacterial origin / cellular response to hydrogen peroxide / negative regulation of inflammatory response / kinase binding / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / : / cell migration / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 / cellular response to lipopolysaccharide / protease binding / cysteine-type deubiquitinase activity / lysosome / inflammatory response / apoptotic process / proteolysis / DNA binding / extracellular exosome / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Lin, S.-C. / Chung, J.Y. / Lo, Y.-C. / Wu, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Molecular basis for the unique deubiquitinating activity of the NF-kappaB inhibitor A20 Authors: Lin, S.-C. / Chung, J.Y. / Lamothe, B. / Rajashankar, K. / Lu, M. / Lo, Y.-C. / Lam, A.Y. / Darnay, B.G. / Wu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dkb.cif.gz | 443.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dkb.ent.gz | 359 KB | Display | PDB format |
PDBx/mmJSON format | 3dkb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/3dkb ftp://data.pdbj.org/pub/pdb/validation_reports/dk/3dkb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 45669.230 Da / Num. of mol.: 6 / Fragment: UNP residues 1-370 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: P21580, Hydrolases |
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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: 2.3 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1 M ammonium sulfate, 300 mM Na thiocyanate, 5 mM MgSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Redundancy: 6.2 % / Av σ(I) over netI: 7.8 / Number: 320586 / Rmerge(I) obs: 0.073 / Χ2: 0.79 / D res high: 2.9 Å / D res low: 50 Å / Num. obs: 51589 / % possible obs: 95.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection twin | Type: hemihedral / Operator: h+k,-k,-l / Fraction: 0.476 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→30 Å / Num. obs: 84504 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.072 / Χ2: 1.202 / Net I/σ(I): 12.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing set |
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Phasing MAD | D res high: 3.5 Å / D res low: 20 Å / FOM : 0.46 / Reflection: 15804 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD set |
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Phasing MAD set site |
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Phasing MAD shell |
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Phasing dm | FOM : 0.74 / FOM acentric: 0.73 / FOM centric: 0.81 / Reflection: 15804 / Reflection acentric: 14730 / Reflection centric: 1074 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→25 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 62.028 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 198.05 Å2 / Biso mean: 69.949 Å2 / Biso min: 6.74 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
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LS refinement shell |
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Xplor file | Serial no: 1 / Param file: CNS_TOPPAR:protein_rep.param |