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- PDB-1ljv: Bovine Pancreatic Polypeptide Bound to DPC Micelles -

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Basic information

Entry
Database: PDB / ID: 1ljv
TitleBovine Pancreatic Polypeptide Bound to DPC Micelles
ComponentsPANCREATIC HORMONE
KeywordsHORMONE/GROWTH FACTOR / NMR micelle peptide hormone / HORMONE-GROWTH FACTOR COMPLEX
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
Pancreatic polypeptide prohormone
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / simulated annealing restraint energy minimization with explicit water
AuthorsLerch, M. / Gafner, V. / Bader, R. / Christen, B. / Zerbe, O.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Bovine pancreatic polypeptide (bPP) undergoes significant changes in conformation and dynamics upon binding to DPC micelles.
Authors: Lerch, M. / Gafner, V. / Bader, R. / Christen, B. / Folkers, G. / Zerbe, O.
History
DepositionApr 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PANCREATIC HORMONE


Theoretical massNumber of molelcules
Total (without water)4,2291
Polymers4,2291
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 / 100structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide PANCREATIC HORMONE / Pancreatic polypeptide / PP


Mass: 4228.745 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pUBK19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01302

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
122E-COSY

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Sample preparation

DetailsContents: 3MM bPP, 300MM D-38 DPC / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 5.5 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
XEASY1.53C. Bartelsdata analysis
DYANA1.5P. Guentertstructure solution
Amber6P. Kollmanrefinement
RefinementMethod: simulated annealing restraint energy minimization with explicit water
Software ordinal: 1
Details: 441 NOE-based distance restraints, 137 torsion angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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