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- PDB-2jvc: NMR solution structure of ubiquitin like protein -

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Basic information

Entry
Database: PDB / ID: 2jvc
TitleNMR solution structure of ubiquitin like protein
Componentsubiquitin_like protein
KeywordsUNKNOWN FUNCTION / ubiquitin
Function / homologyPhosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Function and homology information
MethodSOLUTION NMR / distance geometry
AuthorsTran, N.B. / Liu, Y. / Hew, L.C.
CitationJournal: To be Published
Title: NMR solution structure of ubiquitin like protein
Authors: Tran, N.B. / Liu, Y. / Hew, L.C.
History
DepositionSep 17, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ubiquitin_like protein


Theoretical massNumber of molelcules
Total (without water)8,9371
Polymers8,9371
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)10 / 300target function
RepresentativeModel #1fewest violations

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Components

#1: Protein ubiquitin_like protein


Mass: 8937.221 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The peptide is from recombinant technology.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D CBCA(CO)NH
1223D HN(CA)CB
1313D 1H-15N NOESY
1433D 1H-13C NOESY
1512D 1H-15N HSQC
1622D 1H-13C HSQC
1723D C(CO)NH
1823D H(CCO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-99% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-99% 13C; U-99% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-99% 13C; U-99% 15N] protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMubiquitin like protein[U-99% 15N]1
1.0 mMubiquitin like protein[U-99% 13C; U-99% 15N]2
1.0 mMubiquitin like protein[U-99% 13C; U-99% 15N]3
Sample conditionsIonic strength: 20mM phosphate buffer / pH: 5.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler, Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler, Wuthrichrefinement
NMRPipe2004Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.2.2Johnson, One Moon Scientificdata analysis
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 10

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