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- PDB-1z99: Solution structure of Crotamine, a myotoxin from Crotalus durissu... -

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Basic information

Entry
Database: PDB / ID: 1z99
TitleSolution structure of Crotamine, a myotoxin from Crotalus durissus terrificus
ComponentsCrotamine
KeywordsTOXIN / beta-defensin-fold / myotoxin
Function / homology
Function and homology information


envenomation resulting in occlusion of the pore of voltage-gated potassium channel in another organism / potassium channel regulator activity / defense response to fungus / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Myotoxin / Myotoxin, crotamine / Myotoxins signature. / Myotoxins family profile. / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Crotamine / Crotamine
Similarity search - Component
Biological speciesCrotalus durissus terrificus (tropical rattlesnake)
MethodSOLUTION NMR / OPALp
AuthorsFadel, V. / Bettendorff, P. / Herrmann, T. / de Azevedo, W.F. / Oliveira, E.B. / Yamane, T. / Wuthrich, K.
CitationJournal: Toxicon / Year: 2005
Title: Automated NMR structure determination and disulfide bond identification of the myotoxin crotamine from Crotalus durissus terrificus.
Authors: Fadel, V. / Bettendorff, P. / Herrmann, T. / de Azevedo, W.F. / Oliveira, E.B. / Yamane, T. / Wuthrich, K.
History
DepositionApr 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: 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
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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crotamine


Theoretical massNumber of molelcules
Total (without water)4,9031
Polymers4,9031
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Crotamine / Crt / Myotoxin


Mass: 4902.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Crotalus durissus terrificus (tropical rattlesnake)
Species: Crotalus durissus / Strain: terrificus / References: UniProt: P01475, UniProt: Q9PWF3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8 mM Crotamine, 1uM NaN3, H2O 95%, D2O 5%H2O 95%, D2O 5%
20.9 mM Crotamine, 1uM NaN3, D2O 100 %D2O 100 %
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.8 ambient 293.4 K
25.8 ambient 313.4 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA6.02Güntert P., Herrmann, T.structure solution
RADAR0.9bHerrmann, T.structure solution
CARA1Keller, R.data analysis
XwinNMR3.5Brukercollection
RADAR0.9bHerrmann, T.refinement
RefinementMethod: OPALp / Software ordinal: 1
Details: restrained energy-minimized in a water shell using AMBER force field
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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