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- PDB-2n2s: NMR solution structure of the pheromone Ep-1 from Euplotes petzi -

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Basic information

Entry
Database: PDB / ID: 2n2s
TitleNMR solution structure of the pheromone Ep-1 from Euplotes petzi
Componentspheromone Ep-1
KeywordsSIGNALING PROTEIN / WATER-BORNE PHEROMONE / ALPHA-HELICAL PROTEIN / DISULPHIDE-RICH PROTEIN
Function / homologyPheromone Ep-1
Function and homology information
Biological speciesEuplotes petzi (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsPedrini, B. / Vallesi, A. / Alimenti, C. / Luporini, P.
CitationJournal: To be Published
Title: NMR solution structure of the pheromone Ep-1 from Euplotes petzi
Authors: Vallesi, A. / Alimenti, C. / Pedrini, B. / Luporini, P.
History
DepositionMay 13, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / 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_spectrometer.model
Revision 1.2Nov 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pheromone Ep-1


Theoretical massNumber of molelcules
Total (without water)3,1811
Polymers3,1811
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 / 30structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide pheromone Ep-1


Mass: 3180.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Harvested in 2005 at Adelie Cove, Terra Nova Bay (Ross Sea, Antarctica), S74 46'/E164 00'
Source: (natural) Euplotes petzi (eukaryote) / Strain: Ad-Cov3 / References: UniProt: A0A182DV16*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.25 mM Ep, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.25 mM / Component: Ep-1-1
Sample conditionsIonic strength: 0.06 / pH: 6 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, A.T. et al.refinement
ATNOSHerrmann, T. et al.peak picking
CANDIDHerrmann, T. et al.chemical shift assignment
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 372 / NOE intraresidue total count: 71 / NOE long range total count: 61 / NOE medium range total count: 130 / NOE sequential total count: 110
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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