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- PDB-2jta: NMR structure of immunosuppressory ubiquitin fragment is similar ... -

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Basic information

Entry
Database: PDB / ID: 2jta
TitleNMR structure of immunosuppressory ubiquitin fragment is similar to related ubiquitin region.
Components10-mer ubiquitin peptide
KeywordsSIGNALING PROTEIN / alpha helix / immunosuppression / ubiquitin
MethodSOLUTION NMR / simulated annealing
AuthorsJaremko, M. / Jaremko, L. / Zhukov, I. / Cebrat, M.
CitationJournal: Biopolymers / Year: 2009
Title: The immunosuppressive activity and solution structures of ubiquitin fragments.
Authors: Jaremko, L. / Jaremko, M. / Pasikowski, P. / Cebrat, M. / Stefanowicz, P. / Lisowski, M. / Artym, J. / Zimecki, M. / Zhukov, I. / Szewczuk, Z.
History
DepositionJul 21, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: 10-mer ubiquitin peptide


Theoretical massNumber of molelcules
Total (without water)1,1691
Polymers1,1691
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/peptide 10-mer ubiquitin peptide


Mass: 1169.221 Da / Num. of mol.: 1 / Fragment: 10-residue fragment of ubiquitin / Source method: obtained synthetically / Details: Solid-phase peptide synthesis, FMOC strategy

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-13C HSQC
1312D 1H-1H ROESY

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Sample preparation

DetailsContents: 3.0 mM peptide, methanol / Solvent system: methanol
SampleConc.: 3.0 mM / Component: peptide
Sample conditionsIonic strength: 0.15 / pH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian UnityPlus / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
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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