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- PDB-2ki0: NMR Structure of a de novo designed beta alpha beta -

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Basic information

Entry
Database: PDB / ID: 2ki0
TitleNMR Structure of a de novo designed beta alpha beta
ComponentsDS119
KeywordsDE NOVO PROTEIN / beta-alpha-beta
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsLiang, H. / Chen, H. / Fan, K. / Wei, P. / Guo, X. / Jin, C. / Zeng, C. / Tang, C. / Lai, L.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: De novo design of a beta alpha beta motif.
Authors: Liang, H. / Chen, H. / Fan, K. / Wei, P. / Guo, X. / Jin, C. / Zeng, C. / Tang, C. / Lai, L.
History
DepositionApr 18, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 20, 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_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: DS119


Theoretical massNumber of molelcules
Total (without water)4,0371
Polymers4,0371
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 DS119


Mass: 4036.613 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was prepared by Invitrogen plasmid pGEX-4T-1. The vector was transformed into E. coli.

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1 mM DS119-1, 40 mM sodium phosphate-2, 10 % D2O-3, 90%H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMDS119-11
40 mMsodium phosphate-21
10 %D2O-31
Sample conditionspH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 400 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: molecular dynamics, 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 / Representative conformer: 1

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