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- PDB-3zjg: A20 OTU domain with irreversibly oxidised Cys103 from 60 min H2O2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zjg | ||||||
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Title | A20 OTU domain with irreversibly oxidised Cys103 from 60 min H2O2 soak. | ||||||
![]() | (TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3) x 2 | ||||||
![]() | HYDROLASE / UBIQUITIN / DEUBIQUITINATING ENZYME / REVERSIBLE OXIDATION / SULPHENIC ACID / SULPHINIC ACID / SULPHONIC ACID / CYS PROTEASE | ||||||
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 chronic inflammatory response ...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 chronic inflammatory response / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / protein K11-linked deubiquitination / negative regulation of toll-like receptor 2 signaling pathway / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / 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 / protein K63-linked deubiquitination / positive regulation of hepatocyte proliferation / Transferases; Acyltransferases; Aminoacyltransferases / negative regulation of bone resorption / protein deubiquitination / TNFR1-induced proapoptotic signaling / negative regulation of interleukin-1 beta production / K63-linked deubiquitinase activity / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-2 production / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of interleukin-6 production / response to muramyl dipeptide / negative regulation of tumor necrosis factor production / positive regulation of Wnt signaling pathway / protein K48-linked ubiquitination / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of canonical NF-kappaB signal transduction / cytoskeleton organization / 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 / Regulation of TNFR1 signaling / negative regulation of smooth muscle cell proliferation / NOD1/2 Signaling Pathway / response to molecule of bacterial origin / kinase binding / negative regulation of inflammatory response / cellular response to hydrogen peroxide / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / Ovarian tumor domain proteases / cell migration / protease binding / cellular response to lipopolysaccharide / ubiquitinyl hydrolase 1 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kulathu, Y. / Garcia, F.J. / Mevissen, T.E.T. / Busch, M. / Arnaudo, N. / Carroll, K.S. / Barford, D. / Komander, D. | ||||||
![]() | ![]() Title: Regulation of A20 and Other Otu Deubiquitinases by Reversible Oxidation Authors: Kulathu, Y. / Garcia, F.J. / Mevissen, T.E.T. / Busch, M. / Arnaudo, N. / Carroll, K.S. / Barford, D. / Komander, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 283.2 KB | Display | ![]() |
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PDB format | ![]() | 228.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3zjdC ![]() 3zjeC ![]() 3zjfC ![]() 2vfjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43165.504 Da / Num. of mol.: 1 / Fragment: OTU DOMAIN, RESIDUES 1-366 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THE CATALYTIC CYS103 IS IRREVERSIBLY OXIDISED AND MODELLED AS CYS SULPHINIC ACID (SO2H) Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P21580, ubiquitinyl hydrolase 1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||||
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#2: Protein | Mass: 43181.504 Da / Num. of mol.: 1 / Fragment: OTU DOMAIN, RESIDUES 1-366 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THE CATALYTIC CYS103 IS IRREVERSIBLY OXIDISED AND MODELLED AS CYS SULPHONIC ACID (SO3H) IN CHAIN B. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P21580, ubiquitinyl hydrolase 1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | MUTATION OF RESIDUE GLY114 TO SER | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 6.2 Details: 2-2.5 M NACL, 0.1 M MES [PH 6-6.7] CRYSTALS WERE SOAKED IN 50 UM H2O2 FOR 60 MIN PRIOR TO FREEZING AND DATA COLLECTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→36.32 Å / Num. obs: 69737 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 31.16 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.92→2.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.9 / % possible all: 94.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VFJ Resolution: 1.92→34 Å / SU ML: 0.21 / σ(F): 1.96 / Phase error: 23.1 / Stereochemistry target values: ML Details: SIDE CHAINS OF SEVERAL RESIDUES WERE NOT MODELLED DUE TO DISORDER. SOME SURFACE LOOPS ARE MISSING FROM THE STRUCTURE. SEVERAL RESIDUES WERE MODELLED WITH OCCUPANCY SET TO 0 OR WITH SIDE CHAINS REMOVED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→34 Å
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Refine LS restraints |
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LS refinement shell |
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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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