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- PDB-2m8b: Solution structure of AhPDF1 from Arabidopsis halleri -

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Basic information

Entry
Database: PDB / ID: 2m8b
TitleSolution structure of AhPDF1 from Arabidopsis halleri
Componentsplant defensin PDF1.1
KeywordsPLANT PROTEIN / CSab / 4 disulfide bridges / plant defensin
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
Putative plant defensin PDF1.1
Similarity search - Component
Biological speciesArabidopsis halleri (plant)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsMeindre, F. / Paquet, F. / Landon, C.
CitationJournal: Biochemistry / Year: 2014
Title: The nuclear magnetic resonance solution structure of the synthetic AhPDF1.1b plant defensin evidences the structural feature within the gamma-motif.
Authors: Meindre, F. / Lelievre, D. / Loth, K. / Mith, O. / Aucagne, V. / Berthomieu, P. / Marques, L. / Delmas, A.F. / Landon, C. / Paquet, F.
History
DepositionMay 13, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: plant defensin PDF1.1


Theoretical massNumber of molelcules
Total (without water)5,7001
Polymers5,7001
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)10 / 500structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein plant defensin PDF1.1


Mass: 5699.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis halleri (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: Q29SA6
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1412D 1H-15N HSQC
1512D 1H-13C HSQC
2622D 1H-1H TOCSY
2722D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM AhPDF1, 90% H2O/10% D2O90% H2O/10% D2O
21.3 mM AhPDF1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.3 mMentity-11
1.3 mMentity-22
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
104.5ambient 298 K
204.5ambient 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CCPNMR2.2.2CCPNchemical shift assignment
CCPNMR2.2.2CCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 500 / Conformers submitted total number: 10

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