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- PDB-3zjd: A20 OTU domain in reduced, active state at 1.87 A resolution -

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Basic information

Entry
Database: PDB / ID: 3zjd
TitleA20 OTU domain in reduced, active state at 1.87 A resolution
ComponentsA20P50
KeywordsHYDROLASE / UBIQUITIN / DEUBIQUITINATING ENZYME / REVERSIBLE OXIDATION / SULPHENIC ACID / CYS PROTEASE
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 / tolerance induction to lipopolysaccharide / negative regulation of osteoclast proliferation / negative regulation of CD40 signaling pathway / negative regulation of B cell activation / negative regulation of toll-like receptor 3 signaling pathway / 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 / tolerance induction to lipopolysaccharide / negative regulation of osteoclast proliferation / negative regulation of CD40 signaling pathway / negative regulation of B cell activation / negative regulation of toll-like receptor 3 signaling pathway / negative regulation of chronic inflammatory response / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / 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 toll-like receptor 4 signaling pathway / 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 / regulation of germinal center formation / positive regulation of hepatocyte proliferation / Transferases; Acyltransferases; Aminoacyltransferases / TNFR1-induced proapoptotic signaling / negative regulation of bone resorption / protein K63-linked deubiquitination / negative regulation of interleukin-1 beta production / negative regulation of interleukin-2 production / K63-linked deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of NF-kappaB transcription factor activity / response to muramyl dipeptide / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / positive regulation of Wnt signaling pathway / protein deubiquitination / negative regulation of endothelial cell apoptotic process / protein K48-linked ubiquitination / 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 / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / Negative regulators of DDX58/IFIH1 signaling / negative regulation of smooth muscle cell proliferation / Regulation of TNFR1 signaling / response to molecule of bacterial origin / NOD1/2 Signaling Pathway / negative regulation of inflammatory response / cellular response to hydrogen peroxide / kinase binding / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / Ovarian tumor domain proteases / cell migration / cellular response to lipopolysaccharide / protease binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / inflammatory response / apoptotic process / DNA binding / extracellular exosome / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / OTU-like cysteine protease / OTU domain / OTU domain profile.
Similarity search - Domain/homology
Tumor necrosis factor alpha-induced protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsKulathu, Y. / Garcia, F.J. / Mevissen, T.E.T. / Busch, M. / Arnaudo, N. / Carroll, K.S. / Barford, D. / Komander, D.
CitationJournal: Nat.Commun. / Year: 2013
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
DepositionJan 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A20P50
B: A20P50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5068
Polymers86,2672
Non-polymers2396
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-55.3 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.690, 68.970, 84.300
Angle α, β, γ (deg.)99.04, 100.09, 96.95
Int Tables number1
Space group name H-MP1

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Components

#1: Protein A20P50 / TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3 / TNF ALPHA-INDUCED PROTEIN 3 / OTU DOMAIN-CONTAINING ...TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3 / TNF ALPHA-INDUCED PROTEIN 3 / OTU DOMAIN-CONTAINING PROTEIN 7C / PUTATIVE DNA-BINDING PROTEIN A20 / ZINC FINGER PROTEIN A20 / A20


Mass: 43133.504 Da / Num. of mol.: 2 / Fragment: OTU DOMAIN, RESIDUES 1-366 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P21580, ubiquitinyl hydrolase 1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 6.2 / Details: 2-2.5 M NACL, 0.1 M MES [PH 6-6.7], 10 MM DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.87→47.84 Å / Num. obs: 73826 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 30.57 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.1
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.6 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VFJ

2vfj


Resolution: 1.87→34.292 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 21.58 / 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.
RfactorNum. reflection% reflection
Rfree0.2168 3706 5 %
Rwork0.1817 --
obs0.1835 73777 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→34.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5187 0 9 253 5449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195392
X-RAY DIFFRACTIONf_angle_d1.7557331
X-RAY DIFFRACTIONf_dihedral_angle_d15.7221985
X-RAY DIFFRACTIONf_chiral_restr0.146829
X-RAY DIFFRACTIONf_plane_restr0.008929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.89460.30451370.24382540X-RAY DIFFRACTION90
1.8946-1.92060.25091400.2392758X-RAY DIFFRACTION95
1.9206-1.9480.24161480.21432675X-RAY DIFFRACTION95
1.948-1.97710.22991430.21142759X-RAY DIFFRACTION95
1.9771-2.0080.25551540.20832703X-RAY DIFFRACTION95
2.008-2.04090.23111320.19572712X-RAY DIFFRACTION95
2.0409-2.07610.24561470.18782786X-RAY DIFFRACTION96
2.0761-2.11380.21511320.18942666X-RAY DIFFRACTION95
2.1138-2.15450.25141570.18452749X-RAY DIFFRACTION96
2.1545-2.19840.25341320.17812761X-RAY DIFFRACTION96
2.1984-2.24620.21781360.17152688X-RAY DIFFRACTION96
2.2462-2.29850.17271370.17542800X-RAY DIFFRACTION96
2.2985-2.35590.21871350.172667X-RAY DIFFRACTION95
2.3559-2.41960.21490.17592749X-RAY DIFFRACTION95
2.4196-2.49080.24371490.18112753X-RAY DIFFRACTION96
2.4908-2.57120.25671620.17912728X-RAY DIFFRACTION96
2.5712-2.6630.1791450.18822714X-RAY DIFFRACTION96
2.663-2.76960.22491400.1862729X-RAY DIFFRACTION95
2.7696-2.89560.24851430.19342734X-RAY DIFFRACTION96
2.8956-3.04820.21381610.1852699X-RAY DIFFRACTION95
3.0482-3.2390.21431420.19232706X-RAY DIFFRACTION95
3.239-3.48890.21751370.17312731X-RAY DIFFRACTION95
3.4889-3.83960.19491430.16432689X-RAY DIFFRACTION94
3.8396-4.39420.19241400.15332626X-RAY DIFFRACTION92
4.3942-5.53240.19411330.16372451X-RAY DIFFRACTION86
5.5324-34.2980.23591320.22162498X-RAY DIFFRACTION88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.13050.17480.32512.3127-0.59863.50440.0798-0.1235-0.01360.3025-0.0338-0.11820.1022-0.1611-0.04970.1423-0.0349-0.01540.1853-0.00290.1799-18.640725.9576-12.1141
21.5978-0.06670.22232.7939-0.8172.61470.06980.05450.155-0.5308-0.1202-0.0648-0.16070.07020.02570.24370.04780.03570.1802-0.02490.1999-12.408338.11536.9036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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