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Open data
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Basic information
Entry | Database: PDB / ID: 2mdw | ||||||
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Title | NMR structure of a strand-swapped dimer of the WW domain | ||||||
![]() | Designed protein | ||||||
![]() | DE NOVO PROTEIN / Hub-linked / Miniprotein / Disulfide | ||||||
Biological species | artificial gene (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
![]() | Kier, B.L. / Sheffler, W. / Baker, D. | ||||||
![]() | ![]() Title: Covalent Assembly of Homooligomeric Proteins Using Structure-templating Hubs Authors: Kier, B.L. / Sheffler, W. / Baker, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 597.1 KB | Display | ![]() |
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PDB format | ![]() | 520.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 402.3 KB | Display | ![]() |
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Full document | ![]() | 754.4 KB | Display | |
Data in XML | ![]() | 68.8 KB | Display | |
Data in CIF | ![]() | 103.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Details | Dimerization is covalent, via a WXCXW hub.) |
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Components
#1: Protein/peptide | Mass: 3363.869 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) artificial gene (others) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: A "dumbell" or strand-swapped homodimeric WW domain; essentially a disulfide/beta-sheet hub with entire WW domains as end-caps. Designed using a stand-alone version of Foldit. | ||||||||||||
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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 | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 880 / NOE intraresidue total count: 410 / NOE long range total count: 82 / NOE medium range total count: 76 / NOE sequential total count: 182 / Disulfide bond constraints total count: 2 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 33 |