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- PDB-3tmo: The catalytic domain of human deubiquitinase DUBA -

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Basic information

Entry
Database: PDB / ID: 3tmo
TitleThe catalytic domain of human deubiquitinase DUBA
ComponentsOTU domain-containing protein 5
KeywordsHYDROLASE / OTU fold / Deubiquitinase / phosphorylation
Function / homology
Function and homology information


positive regulation of TORC2 signaling / protein K48-linked deubiquitination / deubiquitinase activity / protein K63-linked deubiquitination / neural crest cell differentiation / K48-linked deubiquitinase activity / negative regulation of type I interferon production / K63-linked deubiquitinase activity / protein deubiquitination / positive regulation of TORC1 signaling ...positive regulation of TORC2 signaling / protein K48-linked deubiquitination / deubiquitinase activity / protein K63-linked deubiquitination / neural crest cell differentiation / K48-linked deubiquitinase activity / negative regulation of type I interferon production / K63-linked deubiquitinase activity / protein deubiquitination / positive regulation of TORC1 signaling / Negative regulators of DDX58/IFIH1 signaling / negative regulation of canonical Wnt signaling pathway / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / response to lipopolysaccharide / proteolysis / nucleus / cytosol
Similarity search - Function
Phosphorylase Kinase; domain 1 - #90 / Arc Repressor Mutant, subunit A - #180 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Arc Repressor Mutant, subunit A / Helix non-globular / Papain-like cysteine peptidase superfamily / Special / Phosphorylase Kinase; domain 1 ...Phosphorylase Kinase; domain 1 - #90 / Arc Repressor Mutant, subunit A - #180 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Arc Repressor Mutant, subunit A / Helix non-globular / Papain-like cysteine peptidase superfamily / Special / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
OTU domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsYin, J. / Bosanac, I. / Ma, X. / Hymowitz, S. / Starovasnik, M. / Cochran, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Phosphorylation-dependent activity of the deubiquitinase DUBA.
Authors: Huang, O.W. / Ma, X. / Yin, J. / Flinders, J. / Maurer, T. / Kayagaki, N. / Phung, Q. / Bosanac, I. / Arnott, D. / Dixit, V.M. / Hymowitz, S.G. / Starovasnik, M.A. / Cochran, A.G.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OTU domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)21,5991
Polymers21,5991
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: OTU domain-containing protein 5

A: OTU domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)43,1972
Polymers43,1972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area5250 Å2
ΔGint-21 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.658, 66.658, 82.218
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein OTU domain-containing protein 5 / Deubiquitinating enzyme A / DUBA


Mass: 21598.607 Da / Num. of mol.: 1 / Fragment: catalytic or OTU domain (Residues 172-351) / Mutation: 3.4.19.12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUBA, OTUD5 / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q96G74, ubiquitinyl hydrolase 1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.8 M succinic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2008
RadiationMonochromator: a high resolution Si(311) cut and a lower resolution Si(111)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 22276 / Num. obs: 21875 / % possible obs: 98.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 44.7 Å2 / Rsym value: 0.062 / Net I/σ(I): 19.9
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 1866 / Rsym value: 0.425 / % possible all: 83.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→28.86 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.184 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27615 503 4.8 %RANDOM
Rwork0.24308 ---
obs0.24459 10073 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.351 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.18 Å2-0 Å2
2--0.37 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 0 0 56 1213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211185
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.9091599
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1655139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35724.57170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43415200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.701157
X-RAY DIFFRACTIONr_chiral_restr0.0790.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021938
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7971.5702
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53921130
X-RAY DIFFRACTIONr_scbond_it2.1053483
X-RAY DIFFRACTIONr_scangle_it3.4724.5469
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 39 -
Rwork0.287 756 -
obs--99.87 %

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