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- PDB-1mr4: Solution Structure of NaD1 from Nicotiana alata -

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Basic information

Entry
Database: PDB / ID: 1mr4
TitleSolution Structure of NaD1 from Nicotiana alata
ComponentsNicotiana alata plant defensin 1 (NaD1)
KeywordsPLANT PROTEIN / cysteine-stabilized alpha-beta motif / plant defensin fold
Function / homology
Function and homology information


vacuole / defense response to fungus / defense response / killing of cells of another organism / extracellular region
Similarity search - Function
Defensin, plant / Gamma-thionins family signature. / Gamma-thionin family / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Defensin-like protein
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodSOLUTION NMR / Simulated annealing with torsion angle dynamics, subsequent refinement in CNS
AuthorsLay, F.T. / Schirra, H.J. / Scanlon, M.J. / Anderson, M.A. / Craik, D.J.
CitationJournal: J.MOL.BIOL. / Year: 2003
Title: The Three-dimensional Solution Structure of NaD1, a New Floral Defensin from Nicotiana alata and its Application to a Homology Model of the Crop Defense Protein alfAFP
Authors: Lay, F.T. / Schirra, H.J. / Scanlon, M.J. / Anderson, M.A. / Craik, D.J.
History
DepositionSep 18, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotiana alata plant defensin 1 (NaD1)


Theoretical massNumber of molelcules
Total (without water)5,3151
Polymers5,3151
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 / 50structures with the lowest energy
Representative

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Components

#1: Protein/peptide Nicotiana alata plant defensin 1 (NaD1) / Flower-specific gamma-thionin


Mass: 5315.377 Da / Num. of mol.: 1 / Fragment: residues 1-47 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / Tissue: Flower buds / References: UniProt: P32026
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1322D NOESY
2412D NOESY
3512D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM NaD1, 90%H2O, 10%D2O90% H2O/10% D2O
21mM NaD1, 99.9%D2O99.9%D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11mM 4ambient 298 K
21mM 4ambient 303 K
31mM 4ambient 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker ARXBrukerARX5001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
XEASYBartelsdata analysis
CNS1Brungerstructure solution
CNS1Brungerrefinement
ARIALingedata analysis
RefinementMethod: Simulated annealing with torsion angle dynamics, subsequent refinement in CNS
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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