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Basic information

Entry
Database: PDB / ID: 6oqp
TitleU-AITx-Ate1
ComponentsSER-LYS-TRP-ILE-CYS-ALA-ASN-ARG-SER-VAL-CYS-PRO-ILE
KeywordsANTITUMOR PROTEIN / Sea anemone Cysteine-containing peptide Structure NMR spectroscopy Lipid interactions
Biological speciesActinia tenebrosa (Australian red waratah sea anemone)
MethodSOLUTION NMR / simulated annealing
AuthorsElnahriry, K.A. / Wai, D.C.C. / Norton, R.S.
CitationJournal: Toxicon / Year: 2019
Title: Structural and functional characterisation of a novel peptide from the Australian sea anemone Actinia tenebrosa.
Authors: Elnahriry, K.A. / Wai, D.C.C. / Krishnarjuna, B. / Badawy, N.N. / Chittoor, B. / MacRaild, C.A. / Williams-Noonan, B.J. / Surm, J.M. / Chalmers, D.K. / Zhang, A.H. / Peigneur, S. / Mobli, M. ...Authors: Elnahriry, K.A. / Wai, D.C.C. / Krishnarjuna, B. / Badawy, N.N. / Chittoor, B. / MacRaild, C.A. / Williams-Noonan, B.J. / Surm, J.M. / Chalmers, D.K. / Zhang, A.H. / Peigneur, S. / Mobli, M. / Tytgat, J. / Prentis, P. / Norton, R.S.
History
DepositionApr 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SER-LYS-TRP-ILE-CYS-ALA-ASN-ARG-SER-VAL-CYS-PRO-ILE


Theoretical massNumber of molelcules
Total (without water)1,4791
Polymers1,4791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide SER-LYS-TRP-ILE-CYS-ALA-ASN-ARG-SER-VAL-CYS-PRO-ILE


Mass: 1478.782 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Actinia tenebrosa (Australian red waratah sea anemone)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
222isotropic22D 1H-1H NOESY
131isotropic12D DQF-COSY
141isotropic12D 1H-15N HSQC
151isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.5 mM U-AITx-Ate1, 95% H2O/5% D2O1.5 mM95% H2O/5% D2O
solution21 mM U-AITx-Ate1, 95% H2O/5% D2O1 mM95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMU-AITx-Ate1natural abundance1
1 mMU-AITx-Ate1natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10 mM1.5 mM4 1 atm283 K
20 mM1 mM4.5 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
XPLOR-NIH2.45Schwieters, Kuszewski, Tjandra and Clorerefinement
TopSpin3.5pl7Brukerchemical shift assignment
NMRFAM-SPARKY3.114Lee, W., Tonelli, M., Markley, J.L.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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