+Open data
-Basic information
Entry | Database: PDB / ID: 2mdu | ||||||
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Title | Circular Permutant of the WW Domain with Loop 1 Excised | ||||||
Components | Pin1 WW domain | ||||||
Keywords | ISOMERASE / Circular Permutation / Miniprotein / Dynamics / Folding | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model9 | ||||||
Authors | Kier, B.L. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Circular Permutation of a WW Domain: Folding Still Occurs after Excising the Turn of the Folding-Nucleating Hairpin. Authors: Kier, B.L. / Anderson, J.M. / 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 | 2mdu.cif.gz | 232.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mdu.ent.gz | 193.2 KB | Display | PDB format |
PDBx/mmJSON format | 2mdu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/2mdu ftp://data.pdbj.org/pub/pdb/validation_reports/md/2mdu | 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: 3794.395 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: This miniprotein construct represents a circular permutation of the Pin1 WW domain (loop 1 excision), with some additional mutations for stability and removal of chromophore redundancy. The ...Details: This miniprotein construct represents a circular permutation of the Pin1 WW domain (loop 1 excision), with some additional mutations for stability and removal of chromophore redundancy. The structure is very similar to that of wild-type WW Pin1, except of course for the termini and loop 1. This miniprotein was not designed with native-like ligand-binding function in mind. | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 50 mM sodium phosphate, 0.5 mM DSS, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||
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Sample |
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Sample conditions | Ionic strength: 0.11 / pH: 6.5 / Pressure: ambient / Temperature: 280 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 / Details: Standard Lennard-Jones potential | ||||||||||||||||||||
NMR constraints | NOE constraints total: 473 / NOE intraresidue total count: 222 / NOE long range total count: 118 / NOE medium range total count: 32 / NOE sequential total count: 101 | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 22 |