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- PDB-2m3j: Solution Structure of Marine Sponge-Derived Asteropsin E Which is... -

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Basic information

Entry
Database: PDB / ID: 2m3j
TitleSolution Structure of Marine Sponge-Derived Asteropsin E Which is Highly Resistant to Gastrointestinal Proteases
ComponentsAsteropsin_E
KeywordsTOXIN / KNOTTIN / SPONGE
Function / homologyAsteropsin A
Function and homology information
Biological speciesAsteropus (invertebrata)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsLi, H. / Jung, J.H.
CitationJournal: To be Published
Title: Solution Structure of Marine Sponge-Derived Asteropsin E Which is Highly Resistant to Gastrointestinal Proteases
Authors: Li, H. / Su, M. / Bowling, J.J. / Hamann, M.T. / Jung, J.H.
History
DepositionJan 21, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: 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 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: Asteropsin_E


Theoretical massNumber of molelcules
Total (without water)3,5471
Polymers3,5471
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_E


Mass: 3547.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asteropus (invertebrata) / References: UniProt: I1SB10*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 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 E, methanol / Solvent system: methanol
SampleConc.: 10 mg/mL / Component: Asteropsin E-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
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CYANA2Guntert, Mumenthaler and Wuthrichrefinement
SparkyGoddarddata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 517 / NOE intraresidue total count: 101 / NOE long range total count: 166 / NOE medium range total count: 63 / NOE sequential total count: 187
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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