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- PDB-1ico: SOLUTION STRUCTURE OF DESIGNED BETA-SHEET MINI-PROTEIN TH10BOX -

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Basic information

Entry
Database: PDB / ID: 1ico
TitleSOLUTION STRUCTURE OF DESIGNED BETA-SHEET MINI-PROTEIN TH10BOX
ComponentsTH10BOX
KeywordsDE NOVO PROTEIN / de novo protein design three-stranded beta-sheet mini-protein motif TH motif
MethodSOLUTION NMR / simulated annealing
AuthorsOttesen, J.J. / Imperiali, B.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Design of a discretely folded mini-protein motif with predominantly beta-structure.
Authors: Ottesen, J.J. / Imperiali, B.
History
DepositionApr 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TH10BOX


Theoretical massNumber of molelcules
Total (without water)3,2691
Polymers3,2691
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)42 / 50structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide TH10BOX


Mass: 3268.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This protein was chemically synthesized.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 3.5mM TH10Box, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: unbuffered / pH: 4.7 / Pressure: ambient / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix97biosymprocessing
Felix95biosymdata analysis
Discover95biosymstructure solution
Discover95biosymrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 500 distance restraints generated from 667 experimental NOE crosspeaks. Angular restraints enforced amide bond planarity.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 42

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