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- PDB-1t55: Antibiotic Activity and Structural Analysis of a Scorpion-derived... -

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Basic information

Entry
Database: PDB / ID: 1t55
TitleAntibiotic Activity and Structural Analysis of a Scorpion-derived Antimicrobial peptide IsCT and Its Analogs
ComponentsCytotoxic linear peptide IsCT
KeywordsANTIBIOTIC / coil-helix
Function / homologyother organism cell membrane / monoatomic ion transport / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region / membrane / Cytotoxic linear peptide IsCT
Function and homology information
Biological speciesOpisthacanthus madagascariensis (scorpion)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsLee, K. / Shin, S.Y. / Kim, K. / Lim, S.S. / Hahm, K.S. / Kim, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Antibiotic activity and structural analysis of the scorpion-derived antimicrobial peptide IsCT and its analogs
Authors: Lee, K. / Shin, S.Y. / Kim, K. / Lim, S.S. / Hahm, K.S. / Kim, Y.
History
DepositionMay 2, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Cytotoxic linear peptide IsCT


Theoretical massNumber of molelcules
Total (without water)1,5861
Polymers1,5861
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cytotoxic linear peptide IsCT / IsCT


Mass: 1586.081 Da / Num. of mol.: 1 / Mutation: E7K, G8P, S11K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Opisthacanthus madagascariensis (scorpion)
Tissue: Venom / Production host: Escherichia coli (E. coli) / References: UniProt: Q8MMJ7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1.0mM Peptide; 200mM SDS-d25 / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000.1processing
X-PLOR3.851Brungerstructure solution
DGII2000.1HAVELrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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