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- PDB-5vr1: Structure of a Turripeptide from Unedogemmula bisaya venom -

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Basic information

Entry
Database: PDB / ID: 5vr1
TitleStructure of a Turripeptide from Unedogemmula bisaya venom
ComponentsTurripeptide
KeywordsUNKNOWN FUNCTION
Biological speciesUnedogemmula bisaya (invertebrata)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDaly, N.L. / Imperial, J.S.
CitationJournal: Biochemistry / Year: 2017
Title: Structure and Biological Activity of a Turripeptide from Unedogemmula bisaya Venom.
Authors: Omaga, C.A. / Carpio, L.D. / Imperial, J.S. / Daly, N.L. / Gajewiak, J. / Flores, M.S. / Espino, S.S. / Christensen, S. / Filchakova, O.M. / Lopez-Vera, E. / Raghuraman, S. / Olivera, B.M. / Concepcion, G.P.
History
DepositionMay 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Turripeptide


Theoretical massNumber of molelcules
Total (without water)1,8071
Polymers1,8071
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint0 kcal/mol
Surface area1560 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Turripeptide


Mass: 1807.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Unedogemmula bisaya (invertebrata)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D DQF-COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 1.5 mM ubi3a, 90% H2O/10% D2O / Label: 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mM / Component: ubi3a / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 0 Not defined / Label: 1 / pH: 5 / Pressure: 1 atm / Temperature: 290 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CcpNMRCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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