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- PDB-1sn1: STRUCTURE OF SCORPION NEUROTOXIN BMK M1 -

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Basic information

Entry
Database: PDB / ID: 1sn1
TitleSTRUCTURE OF SCORPION NEUROTOXIN BMK M1
ComponentsPROTEIN (NEUROTOXIN BMK M1)
KeywordsTOXIN / NEUROTOXIN / SODIUM CHANNEL INHIBITOR / SCORPION
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-like toxin BmK M1
Similarity search - Component
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHe, X.L. / Li, H.M. / Liu, X.Q. / Zeng, Z.H. / Wang, D.C.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structures of two alpha-like scorpion toxins: non-proline cis peptide bonds and implications for new binding site selectivity on the sodium channel.
Authors: He, X.L. / Li, H.M. / Zeng, Z.H. / Liu, X.Q. / Wang, M. / Wang, D.C.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal Structure of an Acidic Neurotoxin from Scorpion Buthus Martensii Karsch at 1.85 A Resolution
Authors: Li, H.M. / Wang, D.C. / Zeng, Z.H. / Jin, L. / Hu, R.Q.
#2: Journal: Toxicon / Year: 1996
Title: Two Neurotoxins (Bmk I and Bmk II) from the Venom of the Scorpion Buthus Martensii Karsch-Purification, Amino Acid Sequence and Assessment of Specific Activity
Authors: Ji, Y.H. / Mansuelle, P. / Terakawa, S. / Kopeyan, C.
#3: 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.
#4: 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.
#5: Journal: Dongwuxue Yanjiu / Year: 1989
Title: Purification and Partial Characterization of Several New Neurotoxins from East- Asia Scorpion [Chinese]
Authors: Hu, R.Q. / Wang, M. / Liu, J.N. / Lei, K.J.
#6: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Variant-3 Scorpion Neurotoxin from Centruroides Sculpturatus Ewing, Refined at 1.8 A Resolution
Authors: Almassy, R.J. / Fontecilla-Camps, J.C. / Suddath, F.L. / Bugg, C.E.
#7: 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
DepositionNov 12, 1998Processing site: RCSB
Revision 1.0Nov 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (NEUROTOXIN BMK M1)


Theoretical massNumber of molelcules
Total (without water)7,2351
Polymers7,2351
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.420, 41.090, 23.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (NEUROTOXIN BMK M1) / SCORPION NEUROTOXIN BMK M1 / TOXIN BMK I


Mass: 7235.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mesobuthus martensii (Chinese scorpion) / Organ: TAIL / Secretion: VENOM / References: UniProt: P45697
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Density % sol: 57.3 %
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.3 mg/mlprotein11
20.005 M11HCl
30.07 Msodium phosphate11
4MPD11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: SIEMENS X200B / Detector: AREA DETECTOR / Date: Dec 14, 1991
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→29.3 Å / Num. obs: 8360 / % possible obs: 87.3 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11
Reflection shellResolution: 1.7→1.8 Å / % possible all: 60.2
Reflection
*PLUS
Num. measured all: 20330 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 52.3 %

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BMK M8

Resolution: 1.7→100 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 1.0E-5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.209 840 10 %RANDOM
Rwork0.169 ---
obs-8360 87.3 %-
Displacement parametersBiso mean: 34.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms503 0 0 111 614
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg1.906
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.28
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.999
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.72→1.78 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.336 57 10 %
Rwork0.269 474 -
obs--60.2 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.28
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.999
LS refinement shell
*PLUS
Rfactor Rfree: 0.336 / % reflection Rfree: 10 % / Rfactor Rwork: 0.269

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