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- PDB-5w96: Solution structure of phage derived peptide inhibitor of frizzled... -

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Basic information

Entry
Database: PDB / ID: 5w96
TitleSolution structure of phage derived peptide inhibitor of frizzled 7 receptor
ComponentsFz7 binding peptide
KeywordsPROTEIN BINDING / peptide inhibitor
Biological speciesunidentified (others)
MethodSOLUTION NMR / simulated annealing
AuthorsNile, A.H. / de Sousa e Melo, F. / Mukund, S. / Piskol, R. / Hansen, S. / Zhou, L. / Zhang, Y. / Fu, Y. / Gogol, E.B. / Komuves, L.G. ...Nile, A.H. / de Sousa e Melo, F. / Mukund, S. / Piskol, R. / Hansen, S. / Zhou, L. / Zhang, Y. / Fu, Y. / Gogol, E.B. / Komuves, L.G. / Modrusan, Z. / Angers, S. / Franke, Y. / Koth, C. / Fairbrother, W.J. / Wang, W. / de Sauvage, F.J. / Hannoush, R.N.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: A selective peptide inhibitor of Frizzled 7 receptors disrupts intestinal stem cells.
Authors: Nile, A.H. / de Sousa E Melo, F. / Mukund, S. / Piskol, R. / Hansen, S. / Zhou, L. / Zhang, Y. / Fu, Y. / Gogol, E.B. / Komuves, L.G. / Modrusan, Z. / Angers, S. / Franke, Y. / Koth, C. / ...Authors: Nile, A.H. / de Sousa E Melo, F. / Mukund, S. / Piskol, R. / Hansen, S. / Zhou, L. / Zhang, Y. / Fu, Y. / Gogol, E.B. / Komuves, L.G. / Modrusan, Z. / Angers, S. / Franke, Y. / Koth, C. / Fairbrother, W.J. / Wang, W. / de Sauvage, F.J. / Hannoush, R.N.
History
DepositionJun 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fz7 binding peptide
B: Fz7 binding peptide


Theoretical massNumber of molelcules
Total (without water)3,5122
Polymers3,5122
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area580 Å2
ΔGint-9 kcal/mol
Surface area2830 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Fz7 binding peptide / Fz7


Mass: 1755.986 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 1 mM Fz binding peptide, 10 mM sodium phosphate, 10 % acentonitrile, 90%H2O 10%acetonitrile
Details: 1mM peptide in 10 mM sodium phosphate pH 7.3 10% acentonitrile-d3 90% H2O
Label: Fz_condition / Solvent system: 90%H2O 10%acetonitrile
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMFz binding peptidenatural abundance1
10 mMsodium phosphatenatural abundance1
10 %acentonitrilenatural abundance1
Sample conditionsIonic strength: 10 mM / Label: FzD sample 1 / pH: 7.3 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker ultrashield plus / Manufacturer: Bruker / Model: ultrashield plus / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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