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- PDB-6m5c: Solution structure of avenatide aV1 -

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Basic information

Entry
Database: PDB / ID: 6m5c
TitleSolution structure of avenatide aV1
Componentsavenatide aV1
KeywordsPLANT PROTEIN / cysteine-rich peptide / hevein-like peptide / plant
Biological speciesAvena sativa (oats)
MethodSOLUTION NMR / simulated annealing
AuthorsTay, S.V. / Wong, K.H. / Huang, J.Y. / Fan, J.S. / Yang, D.W. / Tam, J.P.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE-2016-T3-1-003 Singapore
CitationJournal: To Be Published
Title: Solution structure of avenatide aV1
Authors: Fan, J.S. / Tay, S.V. / Wong, K.H. / Huang, J.Y. / Tam, J.P.
History
DepositionMar 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: 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
Revision 1.2Oct 30, 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: avenatide aV1


Theoretical massNumber of molelcules
Total (without water)3,7411
Polymers3,7411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide avenatide aV1


Mass: 3741.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats)
Has protein modificationY

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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 NOESY
121isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution / Contents: 1.0 mM avenatide aV1, 95% H2O/5% D2O / Label: sample_1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.0 mM / Component: avenatide aV1 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: condition_1 / pH: 3.5 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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