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- PDB-2mdw: NMR structure of a strand-swapped dimer of the WW domain -

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Basic information

Entry
Database: PDB / ID: 2mdw
TitleNMR structure of a strand-swapped dimer of the WW domain
ComponentsDesigned protein
KeywordsDE NOVO PROTEIN / Hub-linked / Miniprotein / Disulfide
Biological speciesartificial gene (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKier, B.L. / Sheffler, W. / Baker, D.
CitationJournal: To be Published
Title: Covalent Assembly of Homooligomeric Proteins Using Structure-templating Hubs
Authors: Kier, B.L. / Sheffler, W. / Baker, D.
History
DepositionSep 18, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Designed protein
B: Designed protein


Theoretical massNumber of molelcules
Total (without water)6,7282
Polymers6,7282
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1069.1 Å2
ΔGint-15.1 kcal/mol
Surface area3172 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)33 / 40structures with the lowest energy
RepresentativeModel #1lowest energy
DetailsDimerization is covalent, via a WXCXW hub.)

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Components

#1: Protein/peptide Designed protein


Mass: 3363.869 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) artificial gene (others)
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 50 mM sodium phosphate, 0.5 mM DSS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMsodium phosphate-11
0.5 mMDSS-21
Sample conditionsIonic strength: 0.11 / pH: 6.5 / Pressure: ambient / Temperature: 280 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
FolditBaker et aldesign
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 33

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