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- PDB-2kfq: NMR Structure of FP1 -

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Basic information

Entry
Database: PDB / ID: 2kfq
TitleNMR Structure of FP1
ComponentsFP1
KeywordsDE NOVO PROTEIN / protein
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsAraki, M. / Tamura, A.
CitationJournal: Febs J. / Year: 2009
Title: Solubility-dependent structural formation of a 25-residue, natively unfolded protein, induced by addition of a seven-residue peptide fragment
Authors: Araki, M. / Tamura, A.
History
DepositionFeb 26, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: 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_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: FP1


Theoretical massNumber of molelcules
Total (without water)3,5191
Polymers3,5191
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide FP1 / Transcription factor Sp1


Mass: 3519.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D DQF-COSY
1312D 1H-1H NOESY
1412D 1H-1H TOCSY

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Sample preparation

DetailsContents: 25mM [U-100% 2H] acetic acid-1, 50mM sodium chloride-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMacetic acid-1[U-100% 2H]1
50 mMsodium chloride-21
Sample conditionsIonic strength: 50 / pH: 3 / Pressure: ambient / Temperature: 293.15 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, Braun, Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
SparkyGoddardchemical shift assignment
DYANA1.5Guntert, Braun, Wuthrichrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10 / Representative conformer: 1

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