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- PDB-1myn: SOLUTION STRUCTURE OF DROSOMYCIN, THE FIRST INDUCIBLE ANTIFUNGAL ... -

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Basic information

Entry
Database: PDB / ID: 1myn
TitleSOLUTION STRUCTURE OF DROSOMYCIN, THE FIRST INDUCIBLE ANTIFUNGAL PROTEIN FROM INSECTS, NMR, 15 STRUCTURES
ComponentsDROSOMYCIN
KeywordsSIGNAL PROTEIN / DROSOMYCIN / INSECT IMMUNITY / ANTIFUNGAL / CSALPHA-BETA MOTIF
Function / homology
Function and homology information


antifungal humoral response / defense response to protozoan / defense response to fungus / response to bacterium / defense response / response to wounding / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-negative bacterium / killing of cells of another organism / extracellular space
Similarity search - Function
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 speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED SIMULATED ANNEALING, ENERGY MINIMIZATION
AuthorsLandon, C. / Sodano, P. / Hetru, C. / Hoffmann, J.A. / Ptak, M.
Citation
Journal: Protein Sci. / Year: 1997
Title: Solution structure of drosomycin, the first inducible antifungal protein from insects.
Authors: Landon, C. / Sodano, P. / Hetru, C. / Hoffmann, J. / Ptak, M.
#1: Journal: FEBS Lett. / Year: 1996
Title: Determination of the Disulfide Array of the First Inducible Antifungal Peptide from Insects: Drosomycin from Drosophila Melanogaster
Authors: Michaut, L. / Fehlbaum, P. / Moniatte, M. / Van Dorsselaer, A. / Reichhart, J.M. / Bulet, P.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: Insect Immunity. Septic Injury of Drosophila Induces the Synthesis of a Potent Antifungal Peptide with Sequence Homology to Plant Antifungal Peptides
Authors: Fehlbaum, P. / Bulet, P. / Michaut, L. / Lagueux, M. / Broekaert, W.F. / Hetru, C. / Hoffmann, J.A.
History
DepositionDec 26, 1996Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DROSOMYCIN


Theoretical massNumber of molelcules
Total (without water)4,9061
Polymers4,9061
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)15 / 30NUMBER OF RESIDUAL VIOLATIONS AND INTERNAL GEOMETRY
Representative

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Components

#1: Protein/peptide DROSOMYCIN


Mass: 4905.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Strain: OREGON R / Organ: FRUIT / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41964
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Sample conditionspH: 4 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
DIANAstructure solution
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED SIMULATED ANNEALING, ENERGY MINIMIZATION
Software ordinal: 1
Details: THE 30 BEST STRUCTURES FROM THE 200 GENERATED WITH THE DIANA PROGRAM WERE REFINED WITH A SIMULATED ANNEALING/ENERGY MINIMIZATION PROTOCOL USING THE X-PLOR COMPUTER PROGRAM.
NMR ensembleConformer selection criteria: NUMBER OF RESIDUAL VIOLATIONS AND INTERNAL GEOMETRY
Conformers calculated total number: 30 / Conformers submitted total number: 15

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