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- PDB-2h9x: NMR structure for the CgNa toxin from the sea anemone Condylactis... -

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Basic information

Entry
Database: PDB / ID: 2h9x
TitleNMR structure for the CgNa toxin from the sea anemone Condylactis gigantea
ComponentsToxin CgNa
KeywordsTOXIN / beta sheet
Function / homologyAnthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / nematocyst / Single Sheet / toxin activity / extracellular region / Mainly Beta / Delta-actitoxin-Cgg1a
Function and homology information
Biological speciesCondylactis gigantea (giant Caribbean anemone)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsLopez-Mendez, B. / Perez-Castells, J. / Gimenez-Gallego, G. / Jimenez-Barbero, J.
Citation
Journal: Biochem.J. / Year: 2007
Title: CgNa, a type I toxin from the giant Caribbean sea anemone Condylactis gigantea shows structural similarities to both type I and II toxins, as well as distinctive structural and functional properties(1).
Authors: Salceda, E. / Perez-Castells, J. / Lopez-Mendez, B. / Garateix, A. / Salazar, H. / Lopez, O. / Aneiros, A. / Standker, L. / Beress, L. / Forssmann, W.G. / Soto, E. / Jimenez-Barbero, J. / Gimenez-Gallego, G.
#1: Journal: Toxicon / Year: 2006
Title: A new toxin from the sea anemone Condylactis gigantea with effect on sodium channel inactivation
Authors: Standker, L. / Beress, L. / Garateix, A. / Christ, T. / Ravens, U. / Salceda, E. / Soto, E. / John, H. / Forssmann, W.G. / Aneiros, A.
History
DepositionJun 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin CgNa


Theoretical massNumber of molelcules
Total (without water)5,0571
Polymers5,0571
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Toxin CgNa


Mass: 5056.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Condylactis gigantea (giant Caribbean anemone)
Tissue: tentacles / References: UniProt: P0C280

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1322D TOCSY
1422D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4mM CgNa; 90% H2O, 10% D2O90% H2O/10% D2O
21.4mM CgNa; D2OD2O
Sample conditionspH: 7 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P.GUNTERT ET ALstructure solution
Amber8D.A.PEARLMAN ET ALrefinement
XEASYC.BARTELS ET ALdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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