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- PDB-1iaz: EQUINATOXIN II -

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Basic information

Entry
Database: PDB / ID: 1iaz
TitleEQUINATOXIN II
ComponentsEQUINATOXIN II
KeywordsTOXIN / beta-sandwich
Function / homology
Function and homology information


nematocyst / pore complex assembly / cytolysis in another organism / other organism cell membrane / channel activity / pore complex / monoatomic cation transport / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsAthanasiadis, A. / Anderluh, G. / Macek, P. / Turk, D.
CitationJournal: Structure / Year: 2001
Title: Crystal structure of the soluble form of equinatoxin II, a pore-forming toxin from the sea anemone Actinia equina.
Authors: Athanasiadis, A. / Anderluh, G. / Macek, P. / Turk, D.
History
DepositionMar 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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: EQUINATOXIN II
B: EQUINATOXIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,74813
Polymers39,6912
Non-polymers1,05711
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.620, 129.040, 31.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EQUINATOXIN II / EQTII / TENEBROSIN C


Mass: 19845.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinia equina (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: P61914
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: isopropanol, ammonium sulphate, sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
25 %isopropanol1reservoir
31.3 Mammonium sulfate1reservoir
4100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→14.3 Å / Num. all: 240282 / Num. obs: 27057 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 6.9
Reflection
*PLUS
Num. measured all: 240282

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
MAINrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.9→12 Å / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.235 1348 a random one out of each twenty consecutive in the order
Rwork0.185 --
all0.19 26965 -
obs0.19 27057 -
Displacement parametersBiso mean: 16.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 55 377 3186
Software
*PLUS
Name: MAIN / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.086
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.55

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