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- PDB-2kzr: Solution NMR Structure of Ubiquitin thioesterase OTU1 (EC 3.1.2.-... -

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Basic information

Entry
Database: PDB / ID: 2kzr
TitleSolution NMR Structure of Ubiquitin thioesterase OTU1 (EC 3.1.2.-) from Mus musculus, Northeast Structural Genomics Consortium Target MmT2A
ComponentsUbiquitin thioesterase OTU1
KeywordsHYDROLASE / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


protein K33-linked deubiquitination / protein K29-linked deubiquitination / protein K27-linked deubiquitination / negative regulation of retrograde protein transport, ER to cytosol / Ovarian tumor domain proteases / protein K11-linked deubiquitination / protein K48-linked deubiquitination / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / endoplasmic reticulum unfolded protein response ...protein K33-linked deubiquitination / protein K29-linked deubiquitination / protein K27-linked deubiquitination / negative regulation of retrograde protein transport, ER to cytosol / Ovarian tumor domain proteases / protein K11-linked deubiquitination / protein K48-linked deubiquitination / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / macroautophagy / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / ubiquitin protein ligase binding / zinc ion binding / cytoplasm
Similarity search - Function
Ubiquitin thioesterase OTU1, C-terminal C2H2-type zinc finger / : / OTU1, UBXL domain / OTU-like cysteine protease / OTU domain / OTU domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Papain-like cysteine peptidase superfamily ...Ubiquitin thioesterase OTU1, C-terminal C2H2-type zinc finger / : / OTU1, UBXL domain / OTU-like cysteine protease / OTU domain / OTU domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin thioesterase OTU1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsChitayat, S. / Gutmanas, A. / Lemak, A. / Yee, A. / Bezsonova, I. / Wu, B. / Doherty, R.S. / Semesi, A. / Montelione, G.T. / Arrowsmith, C.H. ...Chitayat, S. / Gutmanas, A. / Lemak, A. / Yee, A. / Bezsonova, I. / Wu, B. / Doherty, R.S. / Semesi, A. / Montelione, G.T. / Arrowsmith, C.H. / Dhe-Paganon, S. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target MmT2A
Authors: Chitayat, S. / Gutmanas, A. / Lemak, A. / Yee, A. / Bezsonova, I. / Wu, B. / Doherty, R.S. / Semesi, A. / Arrowsmith, C.H. / Dhe-Paganon, S.
History
DepositionJun 23, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin thioesterase OTU1


Theoretical massNumber of molelcules
Total (without water)9,3651
Polymers9,3651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin thioesterase OTU1


Mass: 9364.707 Da / Num. of mol.: 1 / Fragment: UBX-like domain 42-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Yod1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK
References: UniProt: Q8CB27, Hydrolases; Acting on ester bonds; Thioester hydrolases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution NMR Structure of Ubiquitin thioesterase OTU1 EC3.1.2.- from Mus musculus, Northeast Structural Genomics Consortium Target MmT2A
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D 1H-13C arom NOESY
1613D HBHA(CO)NH
1713D HNCA
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D (H)CCH-TOCSY
11113D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1.1 mM [U-100% 13C; U-100% 15N] MmT2A, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 1.1 mM / Component: MmT2A-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MOLMOLKoradi, Billeter and Wuthrichdata analysis
MDDGUI1Gutmanas, Arrowsmithprocessing
FMCGUI2.3Lemak, Arrowsmithchemical shift assignment
FMCGUI2.3Lemak, Arrowsmithrefinement
FMCGUI2.3Lemak, Arrowsmithstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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