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- PDB-1jrj: Solution structure of exendin-4 in 30-vol% trifluoroethanol -

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Basic information

Entry
Database: PDB / ID: 1jrj
TitleSolution structure of exendin-4 in 30-vol% trifluoroethanol
ComponentsExendin-4
KeywordsHORMONE/GROWTH FACTOR / Trp-cage / GLP-1 / poly-proII / hydrophobic cluster / HORMONE-GROWTH FACTOR COMPLEX
Function / homologyGlucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / hormone activity / regulation of blood pressure / toxin activity / extracellular region / Exendin-4
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsNeidigh, J.W. / Fesinmeyer, R.M. / Prickett, K.S. / Andersen, N.H.
CitationJournal: Biochemistry / Year: 2001
Title: Exendin-4 and glucagon-like-peptide-1: NMR structural comparisons in the solution and micelle-associated states.
Authors: Neidigh, J.W. / Fesinmeyer, R.M. / Prickett, K.S. / Andersen, N.H.
History
DepositionAug 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exendin-4


Theoretical massNumber of molelcules
Total (without water)4,1921
Polymers4,1921
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)36 / 50structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations
Representative

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Components

#1: Protein/peptide Exendin-4


Mass: 4191.588 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The protein was produced using FMOC synthesis. The sequence occurs naturally in the salivary secretion of Heloderma suspectum (Gila monster).
References: UniProt: P26349

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: 2D NOESYs performed with mixing times of 60, 150 (deuterated medium), 160ms.

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Sample preparation

DetailsContents: Natural abundance
Solvent system: 2mg/ml in pH 5.9 15mM phosphate buffer with 30 vol-% trifluoroethanol added
Sample conditionsIonic strength: 15mM potassium phosphate / pH: 5.9 / Pressure: ambient / Temperature: 280 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 DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBrukercollection
Felix95MSIprocessing
CNS0.9Brungerstructure solution
CNS0.9Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures were calculated using CNS 0.9 with 294 NOE distance constraints, 20 distance constraints from defined torsion angles, and 116 anti-distance constraints. No hydrogen bond constraints were employed.
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 36

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