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- PDB-1jkz: NMR Solution Structure of Pisum sativum defensin 1 (Psd1) -

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Basic information

Entry
Database: PDB / ID: 1jkz
TitleNMR Solution Structure of Pisum sativum defensin 1 (Psd1)
ComponentsDEFENSE-RELATED PEPTIDE 1
KeywordsANTIFUNGAL PROTEIN / PLANT DEFENSIN / CYS-RICH / ANTIFUNGAL
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism
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
Biological speciesPisum sativum (garden pea)
MethodSOLUTION NMR / THE STRUCTURE WAS CALCULATED USING TORSIONAL SIMULATED ANNEALING, THEN MINIMIZED
AuthorsAlmeida, M.S. / Cabral, K.M.S. / Kurtenbach, E. / Almeida, F.C.L. / Valente, A.P.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Solution structure of Pisum sativum defensin 1 by high resolution NMR: plant defensins, identical backbone with different mechanisms of action.
Authors: Almeida, M.S. / Cabral, K.M. / Kurtenbach, E. / Almeida, F.C. / Valente, A.P.
#1: Journal: To be Published
Title: cDNA CLONING AND HETEROLOGOUS EXPRESSION OF FUNCTIONAL CYS-RICH ANTIFUNGAL PROTEIN PSD1 IN THE YEAST PICHIA PASTORIS
Authors: ALMEIDA, M.S. / CABRAL, K.M.S. / MEDEIROS, L.N. / VALENTE, A.P. / ALMEIDA, F.C.L. / KURTENBACH, E.
#2: Journal: Arch.Biochem.Biophys. / Year: 2000
Title: Characterization of two novel defense peptides from pea (Pisum sativum) seeds
Authors: ALMEIDA, M.S. / CABRAL, K.M. / ZINGALI, R.B. / KURTENBACH, E.
History
DepositionJul 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 999SEQUENCE An appropriate sequence database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DEFENSE-RELATED PEPTIDE 1


Theoretical massNumber of molelcules
Total (without water)5,2181
Polymers5,2181
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 / 100structures with the lowest energy
RepresentativeModel #18lowest energy

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Components

#1: Protein/peptide DEFENSE-RELATED PEPTIDE 1 / PSD1


Mass: 5217.923 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM PEA SEEDS / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P81929*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1311H/15N HMQC
1411H/13C HMQC

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Sample preparation

DetailsContents: 1.8 mM PSD1 / Solvent system: 10 mM SODIUM PHOSPHATE BUFFER pH 4
Sample conditionsIonic strength: 10 mM sodium phosphate / pH: 4 / Pressure: AMBIENT / Temperature: 300 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 DRXBrukerDRX6001
Bruker DRXBrukerDRX4002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5BRUKERcollection
NMRView5.2BRUCE A. JOHNSONdata analysis
CNS_SOLVE1AXEL BRUNGERstructure solution
CNS_SOLVE1AXEL BRUNGERrefinement
RefinementMethod: THE STRUCTURE WAS CALCULATED USING TORSIONAL SIMULATED ANNEALING, THEN MINIMIZED
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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