+Open data
-Basic information
Entry | Database: PDB / ID: 2jof | ||||||
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Title | The Trp-cage: Optimizing the Stability of a Globular Miniprotein | ||||||
Components | TRP-CAGE | ||||||
Keywords | DE NOVO PROTEIN / miniprotein / two-state folding / Trp-cage | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / molecular dynamics, simulated annealing | ||||||
Authors | Barua, B. / Andersen, N.H. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jof.cif.gz | 136.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jof.ent.gz | 96.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jof.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/2jof ftp://data.pdbj.org/pub/pdb/validation_reports/jo/2jof | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2088.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.0 mM TRP-CAGE, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1.0 mM / Component: TRP-CAGE |
Sample conditions | Ionic strength: 0.020 / pH: 7.00 / Pressure: ambient / Temperature: 280 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: molecular dynamics, simulated annealing / Software ordinal: 1 / Details: Steepest descent minimization | ||||||||||||||||||||||||
NMR constraints | NOE 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer 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 rms | Distance rms dev: 0.0351 Å / Distance rms dev error: 0.0038 Å |