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- PDB-2nb6: NMR solution structure of PawS Derived Peptide 10 (PDP-10) -

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Basic information

Entry
Database: PDB / ID: 2nb6
TitleNMR solution structure of PawS Derived Peptide 10 (PDP-10)
ComponentsPreproalbumin PawS1
KeywordsPLANT PROTEIN / plant peptide
Function / homologyProtease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Preproalbumin PawS1
Function and homology information
Biological speciesGalinsoga quadriradiata (plant)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsFranke, B.G. / Elliott, A.G. / Mylne, J.S. / Rosengren, K.J.
CitationJournal: Amino Acids / Year: 2017
Title: Natural structural diversity within a conserved cyclic peptide scaffold.
Authors: Elliott, A.G. / Franke, B. / Armstrong, D.A. / Craik, D.J. / Mylne, J.S. / Rosengren, K.J.
History
DepositionJan 24, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _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: Preproalbumin PawS1


Theoretical massNumber of molelcules
Total (without water)1,8171
Polymers1,8171
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 / 50structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Preproalbumin PawS1


Mass: 1817.047 Da / Num. of mol.: 1 / Fragment: residues 37-52 / Source method: obtained synthetically / Details: Solid phase peptide synthesis. / Source: (synth.) Galinsoga quadriradiata (plant) / References: UniProt: A0A023GYI2

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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 1H-1H NOESY
1312D DQF-COSY
1422D 1H-1H TOCSY
1522D 1H-1H NOESY
1622D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
13 mg/mL PawS Derived Peptide 10 (PDP-10), methanol (CD3OH)methanol (CD3OH)
23 mg/mL PawS Derived Peptide 10 (PDP-10), methanol (CD3OD)methanol (CD3OD)
Sample
Conc. (mg/ml)ComponentSolution-ID
3 mg/mLPawS Derived Peptide 10 (PDP-10)-11
3 mg/mLPawS Derived Peptide 10 (PDP-10)-22
Sample conditionsPressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 125 / NOE intraresidue total count: 18 / NOE long range total count: 15 / NOE medium range total count: 27 / NOE sequential total count: 65 / Protein chi angle constraints total count: 1 / Protein phi angle constraints total count: 8 / Protein psi angle constraints total count: 11
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 20

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