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- PDB-2gfr: Solution structure of Amphibian tachykinin Uperolein bound to DPC... -

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Basic information

Entry
Database: PDB / ID: 2gfr
TitleSolution structure of Amphibian tachykinin Uperolein bound to DPC micelles
ComponentsUperolein
KeywordsNEUROPEPTIDE / Helix / 3-10 Helix / Lipid induced Conformation / DPC micelles
Function / homologyTachykinin domain / Tachykinin family / Tachykinin/Neurokinin-like, conserved site / Tachykinin family signature. / tachykinin receptor signaling pathway / neuropeptide signaling pathway / defense response / extracellular region / Uperolein
Function and homology information
MethodSOLUTION NMR / Distance geometry, simulated aneealing (DYANA)
AuthorsDike, A. / Cowsik, S.M.
CitationJournal: J.Struct.Biol. / Year: 2006
Title: Solution structure of amphibian tachykinin Uperolein bound to DPC micelles.
Authors: Dike, A. / Cowsik, S.M.
History
DepositionMar 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_nmr_software / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uperolein


Theoretical massNumber of molelcules
Total (without water)1,2351
Polymers1,2351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Uperolein


Mass: 1235.365 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemical Synthesis. The sequence is naturally found in Uperoleia rugosa (Wrinkled toadlet).
References: UniProt: P08612
Has protein modificationY

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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: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 4.8 mM Uperolein in water (90%H2O, 10%D2O, pH 4.5)
Solvent system: 233mM perdeuterated DPC
Sample conditionsIonic strength: No salts used / pH: 4.5 / Pressure: ambient / Temperature: 305 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, Kstructure solution
XwinNMR3.1BRUKERprocessing
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, Krefinement
RefinementMethod: Distance geometry, simulated aneealing (DYANA) / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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