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- PDB-3zjf: A20 OTU domain with irreversibly oxidised Cys103 from 270 min H2O... -

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Basic information

Entry
Database: PDB / ID: 3zjf
TitleA20 OTU domain with irreversibly oxidised Cys103 from 270 min H2O2 soak.
Components(A20P50) x 2
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 / 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 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 / regulation of defense response to virus by host / protein K48-linked deubiquitination / regulation of tumor necrosis factor-mediated signaling pathway / regulation of germinal center formation / Transferases; Acyltransferases; Aminoacyltransferases / positive regulation of hepatocyte proliferation / protein K63-linked deubiquitination / negative regulation of bone resorption / TNFR1-induced proapoptotic signaling / negative regulation of interleukin-1 beta production / K63-linked deubiquitinase activity / negative regulation of interleukin-2 production / 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 / Regulation of TNFR1 signaling / negative regulation of smooth muscle cell proliferation / NOD1/2 Signaling Pathway / response to molecule of bacterial origin / negative regulation of inflammatory response / kinase binding / cellular response to hydrogen peroxide / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / cell migration / Ovarian tumor domain proteases / protease binding / cellular response to lipopolysaccharide / 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: 2.2 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 1.2Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.3Dec 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_conn / 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_conn.pdbx_leaving_atom_flag / _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)86,4184
Polymers86,3472
Non-polymers712
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-28.9 kcal/mol
Surface area28990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.700, 68.800, 85.000
Angle α, β, γ (deg.)98.44, 100.56, 97.04
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: 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.) 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: 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: 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).
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)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.85 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]. CRYSTALS WERE SOAKED IN 50 UM H2O2 FOR 270 MIN PRIOR TO FREEZING AND DATA COLLECTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→38.18 Å / Num. obs: 45957 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 36.38 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 95.2

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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: 2.2→34.272 Å / SU ML: 0.27 / σ(F): 2 / Phase error: 24.08 / Stereochemistry target values: ML
Details: SIDE CHAINS OF SEVERAL RESIDUES WERE NOT MODELLED DUE TO DISORDER. SOME SURFACE LOOPS ARE MISSING FROM THE STRUCTURE. CYS103 WAS MODELLED AS SULPHINIC AND SULPHONIC ACID IN CHAIN A AND B, ...Details: SIDE CHAINS OF SEVERAL RESIDUES WERE NOT MODELLED DUE TO DISORDER. SOME SURFACE LOOPS ARE MISSING FROM THE STRUCTURE. CYS103 WAS MODELLED AS SULPHINIC AND SULPHONIC ACID IN CHAIN A AND B, RESPECTIVELY. SEVERAL RESIDUES WERE MODELLED WITH WITH OCCUPANCY SET TO 0 OR WITH SIDE CHAINS REMOVED.
RfactorNum. reflection% reflection
Rfree0.2224 2327 5.1 %
Rwork0.1816 --
obs0.1836 45936 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→34.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5136 0 2 133 5271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135339
X-RAY DIFFRACTIONf_angle_d1.3937245
X-RAY DIFFRACTIONf_dihedral_angle_d15.6481965
X-RAY DIFFRACTIONf_chiral_restr0.1813
X-RAY DIFFRACTIONf_plane_restr0.006917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.24490.31151320.25332514X-RAY DIFFRACTION95
2.2449-2.29370.2671460.23892599X-RAY DIFFRACTION95
2.2937-2.34710.26841160.23052560X-RAY DIFFRACTION95
2.3471-2.40570.23721350.22552575X-RAY DIFFRACTION95
2.4057-2.47080.28791390.21372539X-RAY DIFFRACTION95
2.4708-2.54340.27941450.21292615X-RAY DIFFRACTION95
2.5434-2.62550.2721440.2082515X-RAY DIFFRACTION95
2.6255-2.71930.23631290.19532604X-RAY DIFFRACTION95
2.7193-2.82810.24781360.2032570X-RAY DIFFRACTION95
2.8281-2.95680.24811420.19782592X-RAY DIFFRACTION96
2.9568-3.11260.22191510.19252545X-RAY DIFFRACTION95
3.1126-3.30740.22191330.192583X-RAY DIFFRACTION96
3.3074-3.56260.23731270.17472575X-RAY DIFFRACTION95
3.5626-3.92060.20711440.16162591X-RAY DIFFRACTION96
3.9206-4.48690.17711310.14492568X-RAY DIFFRACTION95
4.4869-5.64890.20221460.15512552X-RAY DIFFRACTION95
5.6489-34.2760.18991310.17822512X-RAY DIFFRACTION93
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)
13.1240.19850.22622.9811-0.70574.43250.0521-0.0686-0.14040.3272-0.0222-0.10910.1784-0.2908-0.02210.088-0.066-0.00410.18030.01270.1506-18.421828.4253-13.0677
22.49630.2450.56292.26970.15773.2243-0.01660.14680.2745-0.57530.0038-0.0671-0.562-0.1885-0.0130.3530.10.05220.202-0.00880.2131-12.487841.29636.0549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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