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- PDB-6nom: NMR solution structure of Pisum sativum defensin 2 (Psd2) provide... -

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Basic information

Entry
Database: PDB / ID: 6nom
TitleNMR solution structure of Pisum sativum defensin 2 (Psd2) provides evidence for the presence of hydrophobic surface clusters
ComponentsDefensin-2
KeywordsANTIMICROBIAL PROTEIN / Psd1 / Psd2 / plant defensins / antimicrobial peptides
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 / simulated annealing
AuthorsPinheiro-Aguiar, R. / Amaral, V.S.G. / Bastos, I. / Kurtenbach, E. / Almeida, F.C.L.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)209306/2013-2 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)457773/2014-6 Brazil
CitationJournal: Proteins / Year: 2020
Title: Nuclear magnetic resonance solution structure of Pisum sativum defensin 2 provides evidence for the presence of hydrophobic surface-clusters.
Authors: Pinheiro-Aguiar, R. / do Amaral, V.S.G. / Pereira, I.B. / Kurtenbach, E. / Almeida, F.C.L.
History
DepositionJan 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
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 / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Defensin-2


Theoretical massNumber of molelcules
Total (without water)5,4141
Polymers5,4141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, SD5 similar assembly
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3220 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Defensin-2 / Antifungal protein Psd2 / Defense-related peptide 2


Mass: 5414.161 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Komagataella pastoris (fungus) / References: UniProt: P81930

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-15N HSQC
121anisotropic12D 1H-13C HSQC
131anisotropic13D HN(CA)CB
141anisotropic13D CBCA(CO)NH
151anisotropic13D HNCA
161anisotropic13D HN(CO)CA
171anisotropic13D HNCO
181anisotropic13D HBHA(CO)NH
191anisotropic13D (H)CCH-TOCSY
1101anisotropic12D 1H-13C HSQC aliphatic
1111anisotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [U-13C; U-15N] Psd2, 90% H2O/10% D2O13C and 15N labelPsd2_label90% H2O/10% D2O
solution21 mM Psd2, 90% H2O/10% D2ONo labelPsd2_non_label90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPsd2[U-13C; U-15N]1
1 mMPsd2natural abundance2
Sample conditionsDetails: Both sample / Ionic strength: 0.012 mM / Label: Conditions_sample / pH: 5.0 / Pressure: 1 atm / Temperature: 25 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: TCI cryogenic probe head.

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Aria2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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