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- PDB-2h7z: Crystal structure of irditoxin -

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Basic information

Entry
Database: PDB / ID: 2h7z
TitleCrystal structure of irditoxin
Components
  • Irditoxin subunit A
  • Irditoxin subunit B
KeywordsTOXIN / three-finger toxin / neurotoxin / snake venom
Function / homology
Function and homology information


modulation of receptor activity in another organism / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin and toxin-like protein / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Irditoxin subunit A / Irditoxin subunit B
Similarity search - Component
Biological speciesBoiga irregularis (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å
AuthorsPawlak, J. / Kini, R.M. / Stura, E.A. / Le Du, M.H.
Citation
Journal: Faseb J. / Year: 2009
Title: Irditoxin, a novel covalently linked heterodimeric three-finger toxin with high taxon-specific neurotoxicity.
Authors: Pawlak, J. / Mackessy, S.P. / Sixberry, N.M. / Stura, E.A. / Le Du, M.H. / Menez, R. / Foo, C.S. / Menez, A. / Nirthanan, S. / Kini, R.M.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: Denmotoxin, a three-finger toxin from the colubrid snake Boiga dendrophila (Mangrove Catsnake) with bird-specific activity.
Authors: Pawlak, J. / Mackessy, S.P. / Fry, B.G. / Bhatia, M. / Mourier, G. / Fruchart-Gaillard, C. / Servent, D. / Menez, R. / Stura, E. / Menez, A. / Kini, R.M.
History
DepositionJun 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 5, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Irditoxin subunit A
B: Irditoxin subunit B


Theoretical massNumber of molelcules
Total (without water)17,1122
Polymers17,1122
Non-polymers00
Water7,963442
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.679, 52.106, 45.031
Angle α, β, γ (deg.)90.00, 106.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Irditoxin subunit A


Mass: 8406.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Boiga irregularis (snake) / References: UniProt: A0S864
#2: Protein Irditoxin subunit B


Mass: 8705.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Boiga irregularis (snake) / References: UniProt: A0S865
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% PEG 5000, 100mM NaBr, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.006768 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 2, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006768 Å / Relative weight: 1
ReflectionResolution: 1.1→52 Å / Num. obs: 53091 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.1→1.12 Å / % possible all: 44.4

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data reduction
MLPHAREphasing
REFMAC5.1.24refinement
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.5→45 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.2399 2092 RANDOM
Rwork0.2142 --
obs0.216 41024 -
all-43116 -
Refinement stepCycle: LAST / Resolution: 1.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 0 442 1620
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.011004
X-RAY DIFFRACTIONr_angle_refined_deg1.77049

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