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- PDB-2sn3: STRUCTURE OF SCORPION TOXIN VARIANT-3 AT 1.2 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2sn3
TitleSTRUCTURE OF SCORPION TOXIN VARIANT-3 AT 1.2 ANGSTROMS RESOLUTION
ComponentsSCORPION NEUROTOXIN (VARIANT 3)
KeywordsTOXIN
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular region
Similarity search - Function
Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / 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 ...Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / 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
Biological speciesCentruroides exilicauda (bark scorpion)
MethodX-RAY DIFFRACTION / Resolution: 1.2 Å
AuthorsZhao, B. / Carson, M. / Ealick, S.E. / Bugg, C.E.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Structure of scorpion toxin variant-3 at 1.2 A resolution.
Authors: Zhao, B. / Carson, M. / Ealick, S.E. / Bugg, C.E.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Variant-3 Scorpion Neurotoxin from Centruroides Sculpturatus Ewing, Refined at 1.8 Angstroms Resolution
Authors: Almassy, R.J. / Fontecilla-Camps, J.C. / Suddath, F.L. / Bugg, C.E.
#2: Journal: Trends Biochem.Sci.(Pers. Ed.) / Year: 1981
Title: Architecture of Scorpion Neurotoxins. A Class of Membrane-Binding Proteins
Authors: Fontecilla-Camps, J.C. / Almassy, R.J. / Ealick, S.E. / Suddath, F.L. / Watt, D.D. / Feldmann, R.J. / Bugg, C.E.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1980
Title: Three-Dimensional Structure of a Protein from Scorpion Venom. A New Structural Class of Neurotoxins
Authors: Fontecilla-Camps, J.C. / Almassy, R.J. / Suddath, F.L. / Watt, D.D. / Bugg, C.E.
History
DepositionFeb 20, 1992Processing site: BNL
SupersessionJan 31, 1994ID: 1SN3
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: SCORPION NEUROTOXIN (VARIANT 3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2142
Polymers7,0961
Non-polymers1181
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.070, 41.940, 28.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 59

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Components

#1: Protein SCORPION NEUROTOXIN (VARIANT 3)


Mass: 7096.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Centruroides exilicauda (bark scorpion)
References: UniProt: P01494
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal grow
*PLUS
pH: 7.1 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
366 %(v/v)MPD1reservoirunbuffered
1Tris-buffer protein 1drop
2MPD1drop

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Data collection

Reflection
*PLUS
Num. obs: 18909 / Observed criterion σ(I): 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.2→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.192 17706
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms948 0 0 134 1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.03
X-RAY DIFFRACTIONp_angle_d0.0410.06
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0520.07
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0180.04
X-RAY DIFFRACTIONp_chiral_restr0.1450.2
X-RAY DIFFRACTIONp_singtor_nbd0.1910.5
X-RAY DIFFRACTIONp_multtor_nbd0.4630.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.4060.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.2
X-RAY DIFFRACTIONp_staggered_tor13.1
X-RAY DIFFRACTIONp_orthonormal_tor12.425
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 10 Å / Num. reflection all: 17706 / σ(F): 0 / Rfactor all: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS

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