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- PDB-3dkb: Crystal Structure of A20, 2.5 angstrom -

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Basic information

Entry
Database: PDB / ID: 3dkb
TitleCrystal Structure of A20, 2.5 angstrom
ComponentsTumor necrosis factor, alpha-induced protein 3
KeywordsHYDROLASE / OTU domain / DUB domain / Apoptosis / Cytoplasm / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Protease / Thiol protease / Ubl conjugation pathway / Zinc / Zinc-finger
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 / MAD / Resolution: 2.5 Å
AuthorsLin, S.-C. / Chung, J.Y. / Lo, Y.-C. / Wu, H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Molecular basis for the unique deubiquitinating activity of the NF-kappaB inhibitor A20
Authors: Lin, S.-C. / Chung, J.Y. / Lamothe, B. / Rajashankar, K. / Lu, M. / Lo, Y.-C. / Lam, A.Y. / Darnay, B.G. / Wu, H.
History
DepositionJun 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Tumor necrosis factor, alpha-induced protein 3
D: Tumor necrosis factor, alpha-induced protein 3
E: Tumor necrosis factor, alpha-induced protein 3
F: Tumor necrosis factor, alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)274,0156
Polymers274,0156
Non-polymers00
Water00
1
A: Tumor necrosis factor, alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)45,6691
Polymers45,6691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tumor necrosis factor, alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)45,6691
Polymers45,6691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tumor necrosis factor, alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)45,6691
Polymers45,6691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tumor necrosis factor, alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)45,6691
Polymers45,6691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Tumor necrosis factor, alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)45,6691
Polymers45,6691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Tumor necrosis factor, alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)45,6691
Polymers45,6691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.636, 123.636, 143.043
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 45669.230 Da / Num. of mol.: 6 / Fragment: UNP residues 1-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: P21580, Hydrolases

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 M ammonium sulfate, 300 mM Na thiocyanate, 5 mM MgSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1971
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.97922, 0.97942,0.97166,0.98714
SYNCHROTRONNSLS X4A20.97563
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJan 1, 2006
ADSC QUANTUM 42CCDJan 1, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979221
20.979421
30.971661
40.987141
50.975631
ReflectionRedundancy: 6.2 % / Av σ(I) over netI: 7.8 / Number: 320586 / Rmerge(I) obs: 0.073 / Χ2: 0.79 / D res high: 2.9 Å / D res low: 50 Å / Num. obs: 51589 / % possible obs: 95.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.245099.810.0361.286.6
4.966.2410010.0631.1236.7
4.334.9610010.0581.0736.7
3.944.3310010.0680.8356.7
3.653.9410010.090.6566.8
3.443.6510010.1350.596.8
3.273.4410010.1930.5166.6
3.123.2799.110.2650.4965.8
33.1289.910.3320.4524.5
2.9361.910.40.443.7
Reflection twinType: hemihedral / Operator: h+k,-k,-l / Fraction: 0.476
ReflectionResolution: 2.5→30 Å / Num. obs: 84504 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.072 / Χ2: 1.202 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.543.90.53341831.06499.7
2.54-2.594.20.47742921.08699.9
2.59-2.644.60.41341751.131100
2.64-2.6950.39242351.143100
2.69-2.755.10.34742351.122100
2.75-2.825.20.30942561.088100
2.82-2.895.30.26642001.103100
2.89-2.965.40.21642391.135100
2.96-3.055.50.17342251.173100
3.05-3.155.60.15242011.204100
3.15-3.265.70.12342431.232100
3.26-3.395.70.09842341.279100
3.39-3.555.70.08342081.302100
3.55-3.735.70.06842051.282100
3.73-3.975.70.06142741.358100
3.97-4.275.80.05142201.293100
4.27-4.75.70.04642251.351100
4.7-5.385.70.04342571.271100
5.38-6.765.70.0442211.099100
6.76-305.50.03541761.16498.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
4
Phasing MADD res high: 3.5 Å / D res low: 20 Å / FOM : 0.46 / Reflection: 15804
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
14 wavelength10.97925.53-7.54
14 wavelength20.97945.8-8.4
14 wavelength30.97173.68-4.01
14 wavelength40.98710.82-4.83
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.8730.7580.1110.387
2Se600.0140.9330.0610.658
3Se600.3720.6020.0530.501
4Se600.5390.0890.1110.409
5Se600.6930.2760.0590.486
6Se600.2150.4370.1070.412
7Se600.8590.870.1310.292
8Se600.8680.8340.0830.613
9Se600.0790.9680.1530.559
10Se600.7490.3120.1510.58
11Se600.8490.9710.0190.261
12Se600.1930.4870.0910.514
13Se50.2840.2030.550.1260.218
14Se600.3980.6270.1560.449
15Se600.4270.6470.1510.418
16Se600.5450.1760.0810.52
17Se600.7170.0180.0450.476
18Se600.1940.3140.1140.455
19Se600.5470.2210.1270.322
20Se600.8680.6430.1190.487
21Se600.520.9810.1110.277
22Se600.5170.1950.1360.311
23Se600.3690.3510.0430.491
24Se600.1480.6280.0020.477
25Se600.4920.2920.0080.596
26Se600.0280.6950.0240.299
27Se600.6440.5860.0590.468
28Se600.0170.2560.0490.303
29Se10.5440.3470.1040.057
30Se56.8560.2310.4630.0440.141
Phasing MAD shell
Resolution (Å)FOM Reflection
11.16-200.58889
7.54-11.160.611355
6.04-7.540.611660
5.18-6.040.531969
4.61-5.180.482175
4.19-4.610.422423
3.87-4.190.362576
3.61-3.870.292757
Phasing dmFOM : 0.74 / FOM acentric: 0.73 / FOM centric: 0.81 / Reflection: 15804 / Reflection acentric: 14730 / Reflection centric: 1074
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10-19.9460.850.830.9962753097
6.3-100.840.830.9321561942214
5-6.30.790.780.8526512456195
4.4-50.820.820.8326842516168
3.8-4.40.720.720.7447594501258
3.5-3.80.540.540.5829272785142

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.13phasing
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→25 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 7644 9 %RANDOM
Rwork0.2 ---
obs-79018 93.5 %-
Solvent computationBsol: 62.028 Å2
Displacement parametersBiso max: 198.05 Å2 / Biso mean: 69.949 Å2 / Biso min: 6.74 Å2
Baniso -1Baniso -2Baniso -3
1-8.146 Å20 Å20 Å2
2--8.146 Å20 Å2
3----16.291 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17550 0 0 0 17550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.5-2.610.33167840.3235X-RAY DIFFRACTION8190
2.61-2.750.32388380.2929X-RAY DIFFRACTION9246
2.75-2.920.30939440.276X-RAY DIFFRACTION9544
2.92-3.150.27149660.2577X-RAY DIFFRACTION10121
3.15-3.460.2610760.2265X-RAY DIFFRACTION10386
3.46-3.960.234810530.1933X-RAY DIFFRACTION10504
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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