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- PDB-2jof: The Trp-cage: Optimizing the Stability of a Globular Miniprotein -

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Basic information

Entry
Database: PDB / ID: 2jof
TitleThe Trp-cage: Optimizing the Stability of a Globular Miniprotein
ComponentsTRP-CAGE
KeywordsDE NOVO PROTEIN / miniprotein / two-state folding / Trp-cage
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsBarua, B. / Andersen, N.H.
CitationJournal: Protein Eng.Des.Sel. / Year: 2008
Title: The Trp-cage: optimizing the stability of a globular miniprotein
Authors: Barua, B. / Lin, J.C. / Williams, V.D. / Kummler, P. / Neidigh, J.W. / Andersen, N.H.
History
DepositionMar 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other / Source and taxonomy
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.5May 8, 2024Group: Database references / Category: 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: TRP-CAGE


Theoretical massNumber of molelcules
Total (without water)2,0881
Polymers2,0881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)28 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide TRP-CAGE


Mass: 2088.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1.0 mM TRP-CAGE, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: TRP-CAGE
Sample conditionsIonic strength: 0.02 / pH: 7 / Pressure: ambient / Temperature: 280 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber6Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollrefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
Sparky3.11Goddardchemical shift assignment
NMRDraw2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XwinNMR2.6Bruker Biospincollection
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1 / Details: Steepest descent minimization
NMR constraintsNOE constraints total: 186 / NOE intraresidue total count: 85 / NOE long range total count: 28 / NOE medium range total count: 21 / NOE sequential total count: 52
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 28 / Maximum lower distance constraint violation: -0.2 Å / Maximum upper distance constraint violation: 0.2 Å
NMR ensemble rmsDistance rms dev: 0.0351 Å / Distance rms dev error: 0.0038 Å

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