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- PDB-4bou: Structure of OTUD3 OTU domain -

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Basic information

Entry
Database: PDB / ID: 4bou
TitleStructure of OTUD3 OTU domain
ComponentsOTU DOMAIN-CONTAINING PROTEIN 3
KeywordsHYDROLASE
Function / homology
Function and homology information


protein K6-linked deubiquitination / cysteine-type deubiquitinase activity => GO:0004843 / protein K27-linked deubiquitination / protein K11-linked deubiquitination / protein K48-linked deubiquitination / protein deubiquitination / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of PTEN stability and activity / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 ...protein K6-linked deubiquitination / cysteine-type deubiquitinase activity => GO:0004843 / protein K27-linked deubiquitination / protein K11-linked deubiquitination / protein K48-linked deubiquitination / protein deubiquitination / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of PTEN stability and activity / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / cytosol / cytoplasm
Similarity search - Function
Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
OTU domain-containing protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMevissen, T.E.T. / Hospenthal, M.K. / Geurink, P.P. / Elliott, P.R. / Akutsu, M. / Arnaudo, N. / Ekkebus, R. / Kulathu, Y. / Wauer, T. / El Oualid, F. ...Mevissen, T.E.T. / Hospenthal, M.K. / Geurink, P.P. / Elliott, P.R. / Akutsu, M. / Arnaudo, N. / Ekkebus, R. / Kulathu, Y. / Wauer, T. / El Oualid, F. / Freund, S.M.V. / Ovaa, H. / Komander, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Otu Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis.
Authors: Mevissen, T.E.T. / Hospenthal, M.K. / Geurink, P.P. / Elliott, P.R. / Akutsu, M. / Arnaudo, N. / Ekkebus, R. / Kulathu, Y. / Wauer, T. / El Oualid, F. / Freund, S.M.V. / Ovaa, H. / Komander, D.
History
DepositionMay 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OTU DOMAIN-CONTAINING PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)18,3531
Polymers18,3531
Non-polymers00
Water2,036113
1
A: OTU DOMAIN-CONTAINING PROTEIN 3

A: OTU DOMAIN-CONTAINING PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)36,7072
Polymers36,7072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
Buried area1790 Å2
ΔGint-12.4 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.196, 36.196, 211.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-2055-

HOH

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Components

#1: Protein OTU DOMAIN-CONTAINING PROTEIN 3 / OTUD3


Mass: 18353.455 Da / Num. of mol.: 1 / Fragment: RESIDUES 52-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPINK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLACI / References: UniProt: Q5T2D3, ubiquitinyl hydrolase 1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONTAINS ADDITIONAL GLYCYL PROLINE SEQUENCE AT N-TERMINUS FOLLOWING AFFINITY TAG REMOVAL.

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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: 2.26 Å3/Da / Density % sol: 45.6 % / Description: NONE
Crystal growDetails: 10% PEG 4K, 0.1 M KCL, 0.01 M MGCL2, 50 MM MES PH 6.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627
DetectorType: ADSC CCD / Detector: CCD / Details: MIRROR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.55→42.21 Å / Num. obs: 23429 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 23.66 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.9
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PFY

3pfy


Resolution: 1.55→31.347 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 1204 5.2 %
Rwork0.1746 --
obs0.1771 23319 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→31.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1127 0 0 113 1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051200
X-RAY DIFFRACTIONf_angle_d0.9161629
X-RAY DIFFRACTIONf_dihedral_angle_d14.376455
X-RAY DIFFRACTIONf_chiral_restr0.066171
X-RAY DIFFRACTIONf_plane_restr0.004219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5503-1.61240.33231300.23672415X-RAY DIFFRACTION99
1.6124-1.68570.27921320.21142430X-RAY DIFFRACTION99
1.6857-1.77460.2941290.18932436X-RAY DIFFRACTION99
1.7746-1.88580.22061510.16812447X-RAY DIFFRACTION99
1.8858-2.03140.26771400.15182439X-RAY DIFFRACTION98
2.0314-2.23570.22211410.14612410X-RAY DIFFRACTION98
2.2357-2.55910.21951350.15542473X-RAY DIFFRACTION99
2.5591-3.22370.22791220.19352485X-RAY DIFFRACTION98
3.2237-31.3530.2121240.17472580X-RAY DIFFRACTION98

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