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- PDB-1p68: Solution structure of S-824, a de novo designed four helix bundle -

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Basic information

Entry
Database: PDB / ID: 1p68
TitleSolution structure of S-824, a de novo designed four helix bundle
ComponentsDe novo designed protein S-824
KeywordsDE NOVO PROTEIN / Protein / four helix bundle / de novo design
Function / homologyDesigned four-helix bundle protein / hypothetical protein mp506/mpn330, domain 1 / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsWei, Y. / Kim, S. / Fela, D. / Baum, J. / Hecht, M.H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2003
Title: Solution structure of a de novo protein from a designed combinatorial library.
Authors: Wei, Y. / Kim, S. / Fela, D. / Baum, J. / Hecht, M.H.
History
DepositionApr 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 1.4May 22, 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: De novo designed protein S-824


Theoretical massNumber of molelcules
Total (without water)11,9491
Polymers11,9491
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)15 / 100back calculated data agree with experimental NOESY spectrum
RepresentativeModel #7lowest energy

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Components

#1: Protein De novo designed protein S-824


Mass: 11949.376 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
NMR detailsText: This structure was determined using standard 3D heteronuclear techniques.

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Sample preparation

DetailsContents: 50mM Acetate buffer / Solvent system: 92% H2O, 8% D2O
Sample conditionsIonic strength: 50mM / pH: 4 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 100 / Conformers submitted total number: 15

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