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- PDB-1ayj: DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPH... -

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Basic information

Entry
Database: PDB / ID: 1ayj
TitleDETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPHANUS SATIVUS ANTIFUNGAL PROTEIN 1 (RS-AFP1) BY 1H NMR, 20 STRUCTURES
ComponentsANTIFUNGAL PROTEIN 1
KeywordsFUNGICIDE / PLANT DEFENSIN / CYSTEINE-STABILIZED ALFA/BETA MOTIF
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
Defensin-like protein 1 / Defensin-like protein 1
Similarity search - Component
Biological speciesRaphanus sativus var. niger (Chinese radish)
MethodSOLUTION NMR / DIANA, SIMULATED ANNEALING
AuthorsFant, F. / Borremans, F.A.M.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Determination of the three-dimensional solution structure of Raphanus sativus antifungal protein 1 by 1H NMR.
Authors: Fant, F. / Vranken, W. / Broekaert, W. / Borremans, F.
#1: Journal: Bull.Soc.Chim.Belg. / Year: 1997
Title: Solution Conformation of Raphanus Sativus Antifungal Protein 1 (Rs-Afp1) by 1H Nuclear Magnetic Resonance. Resonance Assignments, Secondary Structure and Global Fold
Authors: Fant, F. / Vranken, W.F. / Martins, J.C. / Borremans, F.A.M.
History
DepositionNov 5, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Dec 25, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_nmr_software ...entity_poly / pdbx_nmr_software / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 23, 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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIFUNGAL PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)5,6861
Polymers5,6861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500LEAST RESTRAINT VIOLATION AND ENERGY
Representative

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Components

#1: Protein ANTIFUNGAL PROTEIN 1 / RS-AFP1


Mass: 5685.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Raphanus sativus var. niger (Chinese radish)
Organ: SEED / Species: Raphanus sativus / Strain: var. niger / References: UniProt: P30231, UniProt: P69241*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121E.COSY
131NOESY
141TOCSY

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Sample preparation

Sample conditionspH: 4.2 / Temperature: 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AM500 / Manufacturer: Bruker / Model: AM500 / Field strength: 500 MHz

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameDeveloperClassification
DiscoverMSI/BIOSYM TECHNOLOGIESrefinement
DIANA/REDACstructure solution
INSIGHTII/DISCOVERstructure solution
RefinementMethod: DIANA, SIMULATED ANNEALING / Software ordinal: 1
Details: SIMULATED ANNEALING PROTOCOL ADOPTED NILGES ET AL. 1988, FEBS LETTERS, VOL. 239, PP129-136. INSIGHT II ALSO WAS USED.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND ENERGY
Conformers calculated total number: 500 / Conformers submitted total number: 20

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