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- PDB-1fjn: SOLUTION STRUCTURE AND ACTIVITY OF THE FOUR DISULFIDE BOND MEDITE... -

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Basic information

Entry
Database: PDB / ID: 1fjn
TitleSOLUTION STRUCTURE AND ACTIVITY OF THE FOUR DISULFIDE BOND MEDITERRANEAN MUSSEL DEFENSIN MGD-1
ComponentsDEFENSIN MGD-1
KeywordsANTIMICROBIAL PROTEIN / Defensin / Cystine stabilized alpha-beta motif / antibacterial / disulfide bond / synthesis
Function / homologyArthropod defensin / Invertebrate defensins family profile. / Defensin, invertebrate/fungal / Knottin, scorpion toxin-like superfamily / defense response to bacterium / innate immune response / extracellular region / Defensin MGD-1
Function and homology information
MethodSOLUTION NMR / distance geometry
AuthorsYang, Y.S.
CitationJournal: Biochemistry / Year: 2000
Title: Solution structure and activity of the synthetic four-disulfide bond Mediterranean mussel defensin (MGD-1).
Authors: Yang, Y.S. / Mitta, G. / Chavanieu, A. / Calas, B. / Sanchez, J.F. / Roch, P. / Aumelas, A.
History
DepositionAug 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 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: DEFENSIN MGD-1


Theoretical massNumber of molelcules
Total (without water)4,4171
Polymers4,4171
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)20 / 50structures with the lowest energy
Representative

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Components

#1: Protein/peptide DEFENSIN MGD-1


Mass: 4417.127 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: MGD-1 WAS OBTAINED BY SOLID PHASE SYNTHESIS BY USING THE FMOC STRATEGY. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN MEDITERRANEAN MUSSEL (MYTILUS GALLOPROVINCIALIS)
References: UniProt: P80571
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D COSY TOCSY NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques. Several data sets were recorded at temperature ranging from 280 to 320 degres Kelvin

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Sample preparation

DetailsContents: 3 mM MGD-1 solution (0.15ml in a Shigemi tube), pH 3.3
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: nd / pH: 3.3 / Pressure: ambient / Temperature: 285 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.1 / Developer: Brunger / Classification: refinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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