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- PDB-1kfp: Solution structure of the antimicrobial 18-residue gomesin -

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Basic information

Entry
Database: PDB / ID: 1kfp
TitleSolution structure of the antimicrobial 18-residue gomesin
ComponentsGOMESIN
KeywordsANTIBIOTIC / hairpin-like / beta-sheet / disulfide bridges
Function / homologydefense response to fungus / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region / Gomesin
Function and homology information
Biological speciesAcanthoscurria gomesiana (spider)
MethodSOLUTION NMR / distance geometry simulated annealing energy minimization
AuthorsMandard, N. / Bulet, P. / Caille, A. / Daffre, S. / Vovelle, F.
Citation
Journal: Eur.J.Biochem. / Year: 2002
Title: The solution structure of gomesin, an antimicrobial cysteine-rich peptide from the spider.
Authors: Mandard, N. / Bulet, P. / Caille, A. / Daffre, S. / Vovelle, F.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Isolation and characterization of gomesin, an 18-residue cysteine-rich defense peptide from the spider Acanthoscurria gomesiana hemocytes with sequence similarities to horseshoe crab ...Title: Isolation and characterization of gomesin, an 18-residue cysteine-rich defense peptide from the spider Acanthoscurria gomesiana hemocytes with sequence similarities to horseshoe crab antimicrobial peptides of the tachyplesin family
Authors: Silva, P.I. / Daffre, S. / Bulet, P.
History
DepositionNov 22, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Polymer sequence / Source and taxonomy
Category: entity_poly / pdbx_entity_src_syn ...entity_poly / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.details ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GOMESIN


Theoretical massNumber of molelcules
Total (without water)2,2801
Polymers2,2801
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 / 200structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Representative

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Components

#1: Protein/peptide GOMESIN


Mass: 2279.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acanthoscurria gomesiana (spider) / References: UniProt: P82358
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
1212D NOESY
131clean-TOCSY
1422D NOESY
152Clean-TOCSY
2612D NOESY
271Clean-TOCSY
NMR detailsText: This solution structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
13.3mM Gomesin90% H2O/10% D2O
23.3mM Gomesin100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13.5ambient 278 K
23.5ambient 285 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
X-PLOR3.1Brungerrefinement
VNMR6.1Varian, Inc.processing
RefinementMethod: distance geometry simulated annealing energy minimization
Software ordinal: 1
Details: The 20 structures are based on a total of 289 restraints, 279 are NOE-derived distance constraints, 4 are used for hydrogen bonds modelling and 6 (i.e. 2x3) are used for disulfide bridge ...Details: The 20 structures are based on a total of 289 restraints, 279 are NOE-derived distance constraints, 4 are used for hydrogen bonds modelling and 6 (i.e. 2x3) are used for disulfide bridge modelling. No dihedral angle restraints used.
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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