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- PDB-2lwu: NMR solution structure of PawS Derived Peptide 7 (PDP-7) -

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Basic information

Entry
Database: PDB / ID: 2lwu
TitleNMR solution structure of PawS Derived Peptide 7 (PDP-7)
ComponentsPawS Derived Peptide 7 (PDP-7)
KeywordsPLANT PROTEIN / plant peptide / PawS derived / cyclic peptide
Function / homologyPawS Derived Peptide 7 (PDP-7)
Function and homology information
MethodSOLUTION NMR / simulated annealing, Torsion-Angle dynamics
AuthorsElliott, A.G. / Mylne, J.S. / Rosengren, K.
CitationJournal: Plant Cell / Year: 2014
Title: Evolutionary origins of a bioactive peptide buried within Preproalbumin.
Authors: Elliott, A.G. / Delay, C. / Liu, H. / Phua, Z. / Rosengren, K.J. / Benfield, A.H. / Panero, J.L. / Colgrave, M.L. / Jayasena, A.S. / Dunse, K.M. / Anderson, M.A. / Schilling, E.E. / Ortiz- ...Authors: Elliott, A.G. / Delay, C. / Liu, H. / Phua, Z. / Rosengren, K.J. / Benfield, A.H. / Panero, J.L. / Colgrave, M.L. / Jayasena, A.S. / Dunse, K.M. / Anderson, M.A. / Schilling, E.E. / Ortiz-Barrientos, D. / Craik, D.J. / Mylne, J.S.
History
DepositionAug 6, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PawS Derived Peptide 7 (PDP-7)


Theoretical massNumber of molelcules
Total (without water)1,5721
Polymers1,5721
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function, favourable non-bonded energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide PawS Derived Peptide 7 (PDP-7)


Type: Cyclic peptide / Class: Enzyme inhibitor / Mass: 1571.821 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: PawS Derived Peptide 7 (PDP-7)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY
1422D 1H-1H TOCSY
1522D 1H-1H NOESY
1622D 1H-13C HSQC
1722D 1H-1H ECOSY

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Sample preparation

Details
Solution-IDContentsSolvent system
13 mg/mL PDP-7, 80% H2O/10% D2O/10% DMSO80% H2O/10% D2O/10% DMSO
23 mg/mL PDP-7, 90% D2O / 10% DMSO90% D2O / 10% DMSO
Sample
Conc. (mg/ml)ComponentSolution-ID
3 mg/mLPDP-7-11
3 mg/mLPDP-7-22
Sample conditionsIonic strength: 0 / pH: 5.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
TopSpin3Bruker Biospinprocessing
XEASYBartels et al.data analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, Torsion-Angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, favourable non-bonded energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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