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- PDB-5nce: Structure of PsDef1 defensin from Pinus sylvestris -

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Basic information

Entry
Database: PDB / ID: 5nce
TitleStructure of PsDef1 defensin from Pinus sylvestris
ComponentsDefensin-1
KeywordsPLANT PROTEIN / Defensin / Plant Defensin / Scotts pine defensin / conformational dynamics / antibacterial activity / amylase inhibition
Function / homology
Function and homology information


defense response to fungus / 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
Biological speciesPinus sylvestris (Scots pine)
MethodSOLUTION NMR
AuthorsKhairutdinov, B.I. / Ermakova, E.A. / Bessolitsyna, E.K. / Toporkova, Y.Y. / Tarasova, N.B. / Kovaleva, V. / Zuev, Y.F. / Nesmelova, I.V.
Funding support Russian Federation, 3items
OrganizationGrant numberCountry
Russian Foundation for Basic Research12-04-01286-a Russian Federation
Russian Foundation for Basic Research15-44-02309 Russian Federation
Russian Foundation for Basic Research15-29-01239 Russian Federation
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: NMR structure, conformational dynamics, and biological activity of PsDef1 defensin from Pinus sylvestris.
Authors: Khairutdinov, B.I. / Ermakova, E.A. / Yusypovych, Y.M. / Bessolicina, E.K. / Tarasova, N.B. / Toporkova, Y.Y. / Kovaleva, V. / Zuev, Y.F. / Nesmelova, I.V.
History
DepositionMar 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 2, 2018Group: Author supporting evidence / Data collection / Experimental preparation
Category: pdbx_audit_support / pdbx_nmr_exptl_sample_conditions
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_exptl_sample_conditions.pressure / _pdbx_nmr_exptl_sample_conditions.pressure_units
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Defensin-1


Theoretical massNumber of molelcules
Total (without water)5,6121
Polymers5,6121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3300 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / -
Representative

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Components

#1: Protein/peptide Defensin-1


Mass: 5611.574 Da / Num. of mol.: 1 / Fragment: UNP residues 34-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pinus sylvestris (Scots pine) / Gene: Def1 / Plasmid: pET-32 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta-gami pLysS B / References: UniProt: A4L7R7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic22D DQF-COSY
121anisotropic22D 1H-1H TOCSY
131anisotropic22D 1H-1H NOESY
141anisotropic12D 1H-1H TOCSY
151anisotropic12D 1H-1H NOESY
161anisotropic12D 1H-13C HSQC
171anisotropic12D 1H-13C HMBC
181anisotropic12D 1H-13C TOCSY-HSQC
192anisotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM PsDef1, 10 mM sodium acetate, 90% H2O/10% D2Osample190% H2O/10% D2O
solution20.7 mM [U-15N] PsDef1, 10 mM sodium acetate, 90% H2O/10% D2Osample290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMPsDef1natural abundance1
10 mMsodium acetatenatural abundance1
0.7 mMPsDef1[U-15N]2
10 mMsodium acetatenatural abundance2
Sample conditionsIonic strength: 0 Not defined / Label: sample condition 1 / pH: 4.5 / PH err: 0.1 / Pressure: ambient atm / Temperature: 306 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE IIIBrukerAVANCE III5003

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
NMR ensembleConformers submitted total number: 15

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