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Open data
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Basic information
Entry | Database: PDB / ID: 2vfj | ||||||
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Title | Structure of the A20 Ovarian Tumour (OTU) domain | ||||||
![]() | TUMOR NECROSIS FACTOR![]() | ||||||
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Function / homology | ![]() 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 / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / negative regulation of chronic inflammatory response / negative regulation of toll-like receptor 4 signaling pathway / regulation of germinal center formation / protein K48-linked deubiquitination / B-1 B cell homeostasis / regulation of defense response to virus by host / regulation of tumor necrosis factor-mediated signaling pathway / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Komander, D. / Barford, D. | ||||||
![]() | ![]() Title: Structure of the A20 Otu Domain and Mechanistic Insights Into Deubiquitination Authors: Komander, D. / Barford, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 526.5 KB | Display | ![]() |
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PDB format | ![]() | 438.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 43103.480 Da / Num. of mol.: 4 / Fragment: OVARIAN TUMOUR (OTU) DOMAIN, RESIDUES 1-366 Source method: isolated from a genetically manipulated source Details: RESIDUES 1-366 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ChemComp-MG / | Sequence details | RESIDUES 1-366 OF A20 SEVERAL RESIDUES WERE MODELLED AS ALA DUE TO DISORDER | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63 % / Description: 3 WAVELENGTH MAD EXPERIMENT |
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Crystal grow![]() | Details: 1.3-1.6 M MAGNESIUM SULPHATE, 0.1 M MES [PH 6.5-6.9] |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.2→50 Å / Num. obs: 36226 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.6 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: NONE Resolution: 3.2→50.286 Å / σ(F): 1.4 / Stereochemistry target values: ML Details: THE ANISO RECORDS CORRESPOND TO TLS FACTORS INCORPORATED BY PHENIX AND NOT ANISOTROPIC REFINEMENT OF INDIVIDUAL ATOMS.
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Refinement step | Cycle: LAST / Resolution: 3.2→50.286 Å
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Refine LS restraints |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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