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- PDB-3pfy: The catalytic domain of human OTUD5 -

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Basic information

Entry
Database: PDB / ID: 3pfy
TitleThe catalytic domain of human OTUD5
ComponentsOTU domain-containing protein 5
KeywordsHYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC / Peptidase C65 Otubain
Function / homology
Function and homology information


positive regulation of TORC2 signaling / deubiquitinase activity / protein K48-linked deubiquitination / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / neural crest cell differentiation / K63-linked deubiquitinase activity / negative regulation of type I interferon production / protein deubiquitination / positive regulation of TORC1 signaling ...positive regulation of TORC2 signaling / deubiquitinase activity / protein K48-linked deubiquitination / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / neural crest cell differentiation / K63-linked deubiquitinase activity / negative regulation of type I interferon production / 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 / response to lipopolysaccharide / cysteine-type deubiquitinase activity / 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 - #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
DI(HYDROXYETHYL)ETHER / OTU domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.702 Å
AuthorsWalker, J.R. / Asinas, A.E. / Crombet, L. / Dong, A. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The catalytic domain of human OTUD5
Authors: Walker, J.R. / Asinas, A.E. / Crombet, L. / Dong, A. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
History
DepositionOct 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: OTU domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8186
Polymers22,3151
Non-polymers5035
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.605, 80.605, 52.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 22315.311 Da / Num. of mol.: 1 / Fragment: OTU DOMAIN (UNP Residues 172-339)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OTUD5 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96G74, ubiquitinyl hydrolase 1

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Non-polymers , 5 types, 109 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE IN THIS ENTRY CORRESPONDS TO ISOFORM 2 OF UNP Q96G74

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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: 1.9 Å3/Da / Density % sol: 35.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2% PEG 400, 2 M AMMONIUM SULFATE, 0.1 M SODIUM HEPES, PH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2010 / Details: SI(111) DOUBLE CRYSTAL MONOCHROMETER
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 19398 / Num. obs: 19398 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.7 % / Rsym value: 0.06 / Net I/σ(I): 65.27
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 19 % / Mean I/σ(I) obs: 17.9 / Num. unique all: 952 / Rsym value: 0.199 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.702→36.08 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.233 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 983 5.1 %RANDOM
Rwork0.1778 ---
obs0.17922 18360 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.262 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.702→36.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1064 0 33 104 1201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211171
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9321582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7485139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25124.62767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15415192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.019156
X-RAY DIFFRACTIONr_chiral_restr0.1150.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021925
X-RAY DIFFRACTIONr_mcbond_it0.9031.5679
X-RAY DIFFRACTIONr_mcangle_it1.68821105
X-RAY DIFFRACTIONr_scbond_it3.1953492
X-RAY DIFFRACTIONr_scangle_it4.8264.5476
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 81 -
Rwork0.186 1342 -
obs--99.79 %
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)
118.96321.0946-5.336345.2171-11.11424.09080.62780.40831.0212-0.9876-0.892-1.91210.05960.1190.26420.41360.00890.00430.10250.10390.418611.24845.87590.8865
28.52584.7811-1.38759.0281-0.27922.69030.110.01290.4566-0.1929-0.09230.372-0.289-0.1736-0.01770.10450.0283-0.01310.0702-0.00620.12124.891335.77785.0118
37.79552.18775.33581.11211.54154.9761-0.0851-0.20030.08950.02660.01370.17570.0215-0.31520.07140.05970.01330.00050.11550.00090.10344.961628.3610.8051
44.1316-0.202-0.53633.39470.38654.5813-0.0379-0.1680.21260.02750.0465-0.0605-0.10790.0743-0.00860.03880.0293-0.00660.05450.00120.020619.112728.220317.6643
57.7196-4.2031-3.44575.95964.27799.496-0.0484-0.11450.25460.10230.2217-0.31140.05420.4596-0.17330.06770.018-0.02420.09730.0020.025626.414124.575520.4552
61.7958-1.7004-3.51223.70464.19167.3626-0.1128-0.44710.22770.05970.6196-0.27850.22611.1155-0.50680.12940.0661-0.02840.319-0.0970.167134.710717.09348.2406
76.06182.18720.76232.94941.33175.9309-0.00730.05140.05960.10760.0690.00410.13560.2201-0.06170.10940.04780.0130.05520.00570.044123.440517.689810.0062
82.1736-2.0871-0.21545.51720.90341.74930.03530.158-0.09550.1253-0.16760.12890.1203-0.0930.13240.06480.00050.01290.06150.00160.04514.713221.13622.8621
913.4268-14.5247-1.793427.1698-7.393311.4792-0.25580.1452-0.82470.08960.07261.18350.6913-0.32820.18320.256-0.11710.04940.14210.01630.288313.515910.20810.3202
103.687-1.3063-0.05113.6653-0.18173.61490.0272-0.00830.0678-0.1281-0.0552-0.0052-0.06430.09480.0280.05420.013-0.0020.05220.00330.014814.188128.71699.3355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A191 - 196
2X-RAY DIFFRACTION2A197 - 207
3X-RAY DIFFRACTION3A208 - 218
4X-RAY DIFFRACTION4A219 - 237
5X-RAY DIFFRACTION5A238 - 248
6X-RAY DIFFRACTION6A249 - 281
7X-RAY DIFFRACTION7A282 - 296
8X-RAY DIFFRACTION8A297 - 313
9X-RAY DIFFRACTION9A314 - 318
10X-RAY DIFFRACTION10A319 - 336

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