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- PDB-7jn6: NMR Solution Structure of plant defensin AtD90 -

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Basic information

Entry
Database: PDB / ID: 7jn6
TitleNMR Solution Structure of plant defensin AtD90
ComponentsDefensin-like protein 204
KeywordsANTIFUNGAL PROTEIN / plant defensin
Function / homologysecretory vesicle / defense response to fungus / killing of cells of another organism / extracellular region / Defensin-like protein 204
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
AuthorsHarvey, P.J. / Craik, D.J.
CitationJournal: J Fungi (Basel) / Year: 2020
Title: Histidine-Rich Defensins from the Solanaceae and Brasicaceae Are Antifungal and Metal Binding Proteins.
Authors: Bleackley, M.R. / Vasa, S. / Harvey, P.J. / Shafee, T.M.A. / Kerenga, B.K. / Soares da Costa, T.P. / Craik, D.J. / Lowe, R.G.T. / Anderson, M.A.
History
DepositionAug 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: citation / database_2 / pdbx_database_status
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _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

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Assembly

Deposited unit
A: Defensin-like protein 204


Theoretical massNumber of molelcules
Total (without water)6,0621
Polymers6,0621
Non-polymers00
Water0
1


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

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Components

#1: Protein Defensin-like protein 204


Mass: 6061.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g05727, F18C1 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q56XB0

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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
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
142isotropic12D 1H-13C HSQC aliphatic
152isotropic12D 1H-1H ECOSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mg/mL peptide, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution21.0 mg/mL peptide, 100% D2Osample_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mg/mLpeptidenatural abundance1
1.0 mg/mLpeptidenatural abundance2
Sample conditionsIonic strength units: Not defined / Label: condition_1 / pH: 4.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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