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- PDB-2rlk: Refined solution structure of porcine peptide YY (PYY) -

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Basic information

Entry
Database: PDB / ID: 2rlk
TitleRefined solution structure of porcine peptide YY (PYY)
ComponentsPeptide YY
KeywordsHORMONE / peptide hormone / helical hairpin / Amidation
Function / homology
Function and homology information


neuropeptide Y receptor binding / neuropeptide hormone activity / feeding behavior / neuropeptide signaling pathway / extracellular space
Similarity search - Function
Pancreatic hormone-like / Pancreatic hormone-like, conserved site / Pancreatic hormone peptide / Pancreatic hormone family signature. / Pancreatic hormone family profile. / Pancreatic hormones / neuropeptide F / peptide YY family
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodSOLUTION NMR / Force-field minimization using AMBER
Model detailsrefined solution structure from 13C, 15N labeled peptide, including restraints derived from RDCs
AuthorsNeumoin, A. / Mares, J. / Lerch-Bader, M. / Bader, R. / Zerbe, O.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Probing the formation of stable tertiary structure in a model miniprotein at atomic resolution: determinants of stability of a helical hairpin
Authors: Neumoin, A. / Mares, J. / Lerch-Bader, M. / Bader, R. / Zerbe, O.
History
DepositionJul 21, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide YY


Theoretical massNumber of molelcules
Total (without water)4,2461
Polymers4,2461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100lowest energy, good geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Peptide YY / PYY / Peptide tyrosine tyrosine


Mass: 4245.690 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: PYY / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P68005

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: refined solution structure from 13C,15N labeled peptide, including restraints derived from RDCs
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H NOESY
1413D 1H-15N TOCSY
1513D 1H-13C NOESY
1612D 1H-15N HSQC
1712D 1H-13C HSQC
1813D 1H-13C NOESY
NMR detailsText: The structure was determined using a combination of NOE and residual dipolar coupling data.

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Sample preparation

DetailsContents: 1mM [U-100% 13C; U-100% 15N] PYY, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: entity / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0 / pH: 4.1 / Pressure: ambient / Temperature: 301 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
TopSpin1.3Bruker Biospinprocessing
CYANA2.1Guntert, Mumenthaler, Wuthrichstructure solution
Amber6refinement
RefinementMethod: Force-field minimization using AMBER / Software ordinal: 1
NMR constraintsNOE constraints total: 381
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy, good geometry / Conformers calculated total number: 100 / Conformers submitted total number: 20

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