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- PDB-2rt4: NMR Structure of designed protein, AF.2A1, (Ensembles) -

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Basic information

Entry
Database: PDB / ID: 2rt4
TitleNMR Structure of designed protein, AF.2A1, (Ensembles)
ComponentsAF.2A1
KeywordsDE NOVO PROTEIN / Artificial protein / chignolin
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsWatanabe, H. / Yamasaki, K. / Honda, S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Tracing primordial protein evolution through structurally guided stepwise segment elongation.
Authors: Watanabe, H. / Yamasaki, K. / Honda, S.
History
DepositionApr 18, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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: AF.2A1


Theoretical massNumber of molelcules
Total (without water)2,7171
Polymers2,7171
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide AF.2A1


Mass: 2716.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1.8 mM AF.2A1-1, 10 mM [U-100% 2H] sodium acetate-d4-2, 5 % [U-100% 2H] D2O-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.8 mMAF.2A1-11
10 mMsodium acetate-d4-2[U-100% 2H]1
5 %D2O-3[U-100% 2H]1
Sample conditionsIonic strength: 10 / pH: 4.5 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR softwareName: CNS / Classification: refinement
RefinementMethod: 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: 20 / Representative conformer: 1

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