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- PDB-1ptx: CRYSTAL STRUCTURE OF TOXIN II FROM THE SCORPION ANDROCTONUS AUSTR... -

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Basic information

Entry
Database: PDB / ID: 1ptx
TitleCRYSTAL STRUCTURE OF TOXIN II FROM THE SCORPION ANDROCTONUS AUSTRALIS HECTOR REFINED AT 1.3 ANGSTROMS RESOLUTION
ComponentsSCORPION TOXIN II
KeywordsTOXIN
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular region
Similarity search - Function
LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-mammal toxin AaH2
Similarity search - Component
Biological speciesAndroctonus australis (Sahara scorpion)
MethodX-RAY DIFFRACTION / Resolution: 1.3 Å
AuthorsFontecilla-Camps, J.C. / Housset, D.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Crystal structure of toxin II from the scorpion Androctonus australis Hector refined at 1.3 A resolution.
Authors: Housset, D. / Habersetzer-Rochat, C. / Astier, J.P. / Fontecilla-Camps, J.C.
#1: Journal: J.Mol.Evol. / Year: 1989
Title: Three-Dimensional Model of the Insect-Directed Scorpion Toxin from Androctonus Australis Hector and its Implication for the Evolution of Scorpion Toxins in General
Authors: Fontecilla-Camps, J.C.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Orthorhombic Crystals and Three-Dimensional Structure of the Potent Toxin II from the Scorpion Androctonus Australis Hector
Authors: Fontecilla-Camps, J.C. / Habersetzer-Rochat, C. / Rochat, H.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1980
Title: Three-Dimensional Structure of a Protein from Scorpion Venom: A New Structural Class of Neurotoxin
Authors: Fontecilla-Camps, J.C. / Almassy, R.J. / Suddath, F.L. / Watt, D.D. / Bugg, C.E.
History
DepositionSep 2, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SCORPION TOXIN II


Theoretical massNumber of molelcules
Total (without water)7,2621
Polymers7,2621
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.940, 40.680, 29.930
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 SCORPION TOXIN II /


Mass: 7262.167 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Androctonus australis (Sahara scorpion)
References: UniProt: P01484
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8 / Method: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mltoxin11
20.2 M11NH4CH3COO

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 9999 Å / Num. all: 14393 / Num. obs: 13619 / % possible obs: 94.6 % / Rmerge(I) obs: 0.12
Reflection shell
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 1.32 Å / % possible obs: 86.1 % / Num. possible: 693 / Num. unique obs: 597

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.3→7 Å / σ(F): 2.5 /
RfactorNum. reflection
Rwork0.148 -
obs0.148 13501
Refinement stepCycle: LAST / Resolution: 1.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms521 0 0 117 638
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.2623
X-RAY DIFFRACTIONx_mcangle_it1.7793.5
X-RAY DIFFRACTIONx_scbond_it2.434
X-RAY DIFFRACTIONx_scangle_it3.475
Software
*PLUS
Name: X-PLOR/PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.148
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.030.028
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_planar_d0.050.047
X-RAY DIFFRACTIONp_plane_restr0.020.018
X-RAY DIFFRACTIONp_chiral_restr0.150.186
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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