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- PDB-5dq6: Mus musculus A20 OTU domain -

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Basic information

Entry
Database: PDB / ID: 5dq6
TitleMus musculus A20 OTU domain
ComponentsTumor necrosis factor alpha-induced protein 3
KeywordsHYDROLASE / A20 OTU
Function / homology
Function and homology information


negative regulation of granuloma formation / TNFR1-induced proapoptotic signaling / 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 CD40 signaling pathway / negative regulation of B cell activation / negative regulation of toll-like receptor 3 signaling pathway / Negative regulators of DDX58/IFIH1 signaling ...negative regulation of granuloma formation / TNFR1-induced proapoptotic signaling / 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 CD40 signaling pathway / negative regulation of B cell activation / negative regulation of toll-like receptor 3 signaling pathway / Negative regulators of DDX58/IFIH1 signaling / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / negative regulation of chronic inflammatory response / TNFR1-induced NF-kappa-B signaling pathway / marginal zone B cell differentiation / Regulation of TNFR1 signaling / Ovarian tumor domain proteases / protein K11-linked deubiquitination / negative regulation of heterotypic cell-cell adhesion / negative regulation of cyclin-dependent protein serine/threonine kinase activity / B-1 B cell homeostasis / NOD1/2 Signaling Pathway / protein K48-linked deubiquitination / positive regulation of hepatocyte proliferation / regulation of germinal center formation / regulation of immunoglobulin production / Transferases; Acyltransferases; Aminoacyltransferases / protein K63-linked deubiquitination / negative regulation of interleukin-1 beta production / negative regulation of interleukin-2 production / regulation of innate immune response / response to muramyl dipeptide / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / 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 / negative regulation of protein ubiquitination / negative regulation of autophagy / negative regulation of innate immune response / ubiquitin binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / response to molecule of bacterial origin / response to wounding / negative regulation of inflammatory response / kinase binding / cellular response to hydrogen peroxide / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / cellular response to lipopolysaccharide / protease binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / inflammatory response / apoptotic process / proteolysis / DNA binding / zinc ion binding / identical protein binding / nucleus / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMabbitt, P.D. / Jackson, C.J.
CitationJournal: To Be Published
Title: Mus musculus A20 OTU domain
Authors: Mabbitt, P.D. / Jackson, C.J.
History
DepositionSep 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor alpha-induced protein 3
B: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)84,2832
Polymers84,2832
Non-polymers00
Water46826
1
A: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)42,1411
Polymers42,1411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)42,1411
Polymers42,1411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.340, 71.340, 143.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Tumor necrosis factor alpha-induced protein 3 / TNF alpha-induced protein 3 / Putative DNA-binding protein A20 / Zinc finger protein A20


Mass: 42141.414 Da / Num. of mol.: 2 / Fragment: OTU domain (UNP residues 1-360)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfaip3, Tnfip3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q60769, ubiquitinyl hydrolase 1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2.4 M NaCl, 0.1 M MES / PH range: 6-6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→37.77 Å / Num. obs: 19279 / % possible obs: 92.1 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.06639 / Net I/σ(I): 11.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZJF

3zjf


Resolution: 2.8→37.77 Å / Cross valid method: FREE R-VALUE / σ(F): 1.65 / Phase error: 40.07 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2905 1077 5.59 %
Rwork0.2527 --
obs0.2555 19279 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5511 0 0 26 5537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115633
X-RAY DIFFRACTIONf_angle_d1.4347607
X-RAY DIFFRACTIONf_dihedral_angle_d16.1952144
X-RAY DIFFRACTIONf_chiral_restr0.06835
X-RAY DIFFRACTIONf_plane_restr0.007965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8006-2.92750.32451270.32012325X-RAY DIFFRACTION93
2.9275-3.08110.38681260.32322321X-RAY DIFFRACTION93
3.0811-3.2730.32021580.30122264X-RAY DIFFRACTION91
3.273-3.52390.39171500.31592248X-RAY DIFFRACTION90
3.5239-3.87510.34981380.30542273X-RAY DIFFRACTION91
3.8751-4.42820.27691380.26162233X-RAY DIFFRACTION89
4.4282-5.55030.2971370.23242217X-RAY DIFFRACTION89
5.5503-17.69850.21991030.19622242X-RAY DIFFRACTION90
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)
12.39620.08960.50578.2506-3.85376.47040.2224-0.3816-0.3645-0.1561-0.0017-1.3411-0.81071.69490.33050.3044-0.3068-0.16781.75650.30940.8102-5.8715-9.1361-14.272
24.2386-0.21590.20489.472-1.5576.32760.13260.1988-0.28040.6868-1.23540.8396-0.18991.81020.46790.50130.0472-0.03240.81380.2050.7094-13.8019-15.0354-8.3584
35.43615.5412-1.95327.0123-2.27869.02060.1420.7576-0.1779-0.4372-0.98910.97690.0662-0.09420.7181.06970.4381-0.36360.7711-0.11811.007-18.4322-33.5523-12.3534
49.1578-1.2034-0.89566.6166-2.04976.95720.6485-0.5457-0.93051.0053-1.5142-0.5388-0.79511.7260.78440.8929-0.118-0.1511.18440.35570.7668-12.5397-20.50630.2763
5-0.34310.09480.46752.10210.50111.35390.3381-0.4052-0.13671.2053-0.6987-0.7356-0.28890.45860.53431.072-0.2349-0.19461.55470.41551.0965-5.3612-21.15675.7466
65.08863.0856-0.37114.4979-0.41522.1240.547-1.47040.74741.8984-1.8880.11870.1780.33190.45761.7542-0.4832-0.70061.40130.20520.724-7.469110.0856-12.127
77.6069-2.6166-2.02046.21940.40815.95310.0960.6565-0.96470.3637-0.59791.26340.5554-0.77270.47270.8651-0.12890.25370.7226-0.10570.860713.78953.049711.9352
86.3374-1.6414-2.00723.5581.40071.2618-1.4456-1.571-0.72731.09980.5502-0.66131.37721.07280.40681.82510.25630.30161.1929-0.23930.694236.157-7.800115.2524
99.9334-2.6-0.28535.58830.70064.9477-0.19310.8317-0.04130.3106-0.27950.04130.6019-0.70230.52541.0406-0.2250.13450.6739-0.13690.625722.8124-0.25394.1701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 202 )
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 285 )
5X-RAY DIFFRACTION5chain 'A' and (resid 286 through 341 )
6X-RAY DIFFRACTION6chain 'A' and (resid 342 through 359 )
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 120 )
8X-RAY DIFFRACTION8chain 'B' and (resid 121 through 145 )
9X-RAY DIFFRACTION9chain 'B' and (resid 146 through 357 )

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