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- PDB-1kd6: Solution structure of the eukaryotic pore-forming cytolysin equin... -

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Basic information

Entry
Database: PDB / ID: 1kd6
TitleSolution structure of the eukaryotic pore-forming cytolysin equinatoxin II
ComponentsEQUINATOXIN II
KeywordsMEMBRANE PROTEIN / cytolysin / pore formation / beta sandwich / toxin / sea anemone
Function / homology
Function and homology information


nematocyst / pore complex assembly / cytolysis in another organism / other organism cell membrane / pore complex / monoatomic cation transport / channel activity / toxin activity / extracellular region
Similarity search - Function
Sea anemone actinoporin-like / : / Sea anemone cytotoxic protein / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta
Similarity search - Domain/homology
DELTA-actitoxin-Aeq1a
Similarity search - Component
Biological speciesActinia equina (sea anemone)
MethodSOLUTION NMR / torsion angle dyanamics distance geometry simulated annealing
AuthorsHinds, M.G. / Zhang, W. / Anderluh, G. / Hansen, P.E. / Norton, R.S.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Solution structure of the eukaryotic pore-forming cytolysin equinatoxin II: implications for pore formation.
Authors: Hinds, M.G. / Zhang, W. / Anderluh, G. / Hansen, P.E. / Norton, R.S.
#1: Journal: J.Biomol.NMR / Year: 2000
Title: Sequence-specific resonance assignments of the potent cytolysin equinatoxin II
Authors: Zhang, W. / Hinds, M.G. / Anderluh, G. / Hansen, P.E. / Norton, R.S.
History
DepositionNov 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE THERE ARE TWO NATURALLY OCCURING SEQUENCE VARIANTS P116D AND T212S FOR EQUINATOXIN II ...SEQUENCE THERE ARE TWO NATURALLY OCCURING SEQUENCE VARIANTS P116D AND T212S FOR EQUINATOXIN II P116D VARIANT OCCURS IN 50% OF MOLECULES FROM ACTINIA EQUINA AND THE T212S VARIANT IN ACTINA TENEBROSA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EQUINATOXIN II


Theoretical massNumber of molelcules
Total (without water)19,8591
Polymers19,8591
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 / 250structures with acceptable covalent geometry,structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein EQUINATOXIN II / EqtII / Tenebrosin C


Mass: 19859.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinia equina (sea anemone) / Plasmid: pAG2.1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61914

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
132HNHA
143NOESY
NMR detailsText: The structure was determined using triple resonance spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM 13C, 15N Equinatoxin II pH 3.990% H2O, 10% H2O
21mM 15N Equinatoxin II pH 3.990% H2O, 10% H2O
31mM unlabelled Equinatoxin II pH 3.990% H2O, 10% H2O
Sample conditionspH: 3.9 / Pressure: ambient / Temperature: 303 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA8003
Bruker DRXBrukerDRX6004

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6Varian Associatescollection
XwinNMR2.6Bruker AGprocessing
XEASY1.3.13Bartels, C., Xia, T.H., Guntert, P., Wuthrich K. J Biomol NMR. 1995, 6, 1-10.data analysis
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, K.J. Mol. Biol. 1997, 273, 283-298.structure solution
CNS1Brunger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S, Read, R.J., Rice, L.M., Simonson, T., Warren, G.L. Acta Crystallogr. D Biol. Crystallogr. 1998, 54, 905-921.refinement
RefinementMethod: torsion angle dyanamics distance geometry simulated annealing
Software ordinal: 1
Details: The structure is based on 3161 total restraints including 167 angle constraints, 42 hydrogen bonds, 534 sequential, 972 short range and 1346 long range distance constraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations
Conformers calculated total number: 250 / Conformers submitted total number: 20

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