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- PDB-2n2g: SOLUTION NMR STRUCTURE of ASTEROPSIN F FROM MARINE SPONGE ASTEROPUS -

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Basic information

Entry
Database: PDB / ID: 2n2g
TitleSOLUTION NMR STRUCTURE of ASTEROPSIN F FROM MARINE SPONGE ASTEROPUS
ComponentsAsteropsin_F
KeywordsTOXIN / KNOTTIN / SPONGE
Function / homologyAsteropsin_F
Function and homology information
Biological speciesAsteropus (invertebrata)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsSu, M. / Jung, J.H.
CitationJournal: To be Published
Title: Stable and non-cytotoxic cystine knot peptides from a marine sponge
Authors: Su, M. / Li, H. / Wang, H. / Kim, E. / Hong, J. / Hamann, M.T. / Kim, H. / Kim, E. / Jung, J.H.
History
DepositionMay 7, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.2Nov 13, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Asteropsin_F


Theoretical massNumber of molelcules
Total (without water)3,5481
Polymers3,5481
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Asteropsin_F


Mass: 3548.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asteropus (invertebrata) / References: UniProt: A0A1A9T938*PLUS
Has protein modificationY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY
1412D 1H-13C HSQC

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Sample preparation

DetailsContents: 10 mg/mL Asteropsin F-1, methanol / Solvent system: methanol
SampleConc.: 10 mg/mL / Component: Asteropsin F-1
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker BioSpin GmbH / Manufacturer: Bruker / Model: BioSpin GmbH / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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