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- PDB-5n9v: NMR solution structure of ubl5 domain from polyubiquitin locus of... -

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Basic information

Entry
Database: PDB / ID: 5n9v
TitleNMR solution structure of ubl5 domain from polyubiquitin locus of T.thermophila.
ComponentsNAD(P)(+)--arginine ADP-ribosyltransferase
KeywordsTRANSFERASE / beta-grasp / ULD / polyubiquitin
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / intein-mediated protein splicing / nucleotidyltransferase activity
Similarity search - Function
Vint domain / Hint-domain / NAD:arginine ADP-ribosyltransferase, ART / NAD:arginine ADP-ribosyltransferase / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region ...Vint domain / Hint-domain / NAD:arginine ADP-ribosyltransferase, ART / NAD:arginine ADP-ribosyltransferase / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
NAD(P)(+)--arginine ADP-ribosyltransferase
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsChiarini, V. / Tossavainen, H.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: NMR structure of a non-conjugatable, ADP-ribosylation associated, ubiquitin-like domain from Tetrahymena thermophila polyubiquitin locus.
Authors: Chiarini, V. / Tossavainen, H. / Sharma, V. / Colotti, G.
History
DepositionFeb 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Sep 25, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(P)(+)--arginine ADP-ribosyltransferase


Theoretical massNumber of molelcules
Total (without water)9,4581
Polymers9,4581
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5750 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NAD(P)(+)--arginine ADP-ribosyltransferase / Mono(ADP-ribosyl)transferase


Mass: 9457.851 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Strain: SB210 / Gene: TTHERM_00085190 / Production host: Escherichia coli (E. coli)
References: UniProt: Q236S9, NAD+-protein-arginine ADP-ribosyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic13D 1H-15N TOCSY
141isotropic13D 1H-15N NOESY
151isotropic23D 1H-13C NOESY
161isotropic13D HNCO
171isotropic13D HN(CA)CB
181isotropic13D HNCA
191isotropic13D CBCA(CO)NH
1101isotropic23D HN(CO)CA
1111isotropic13D HN(CA)CO
1121isotropic23D HCC(CO)NH
1131isotropic23D (H)CCH-COSY

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Sample preparation

DetailsType: solution
Contents: 4 mM [U-13C; U-15N] T.thermophila BUBL1-ubl5, 20 mM sodium phosphate, 90% H2O/10% D2O
Label: 15N-13C / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4 mMT.thermophila BUBL1-ubl5[U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 0.06 M / Label: condition / pH: 6 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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