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- PDB-1snb: STRUCTURE OF SCORPION NEUROTOXIN BMK M8 -

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Basic information

Entry
Database: PDB / ID: 1snb
TitleSTRUCTURE OF SCORPION NEUROTOXIN BMK M8
ComponentsNEUROTOXIN BMK M8
KeywordsNEUROTOXIN / SODIUM CHANNEL INHIBITOR / SCORPION
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 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 BmK-M8
Similarity search - Component
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, D.C. / Zeng, Z.H. / Li, H.M.
Citation
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.
#1: 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.
#2: Journal: Chin.Sci.Bull. / Year: 1993
Title: Crystallographic Studies on an Acidic Toxin from Scorpion Buthus Martensii Karsch
Authors: Jin, L. / Wang, M. / Zeng, Z.H. / Hu, R.Q. / Wang, D.C.
#3: 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.
#4: 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.
#5: 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.
#6: 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
DepositionMar 12, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEUROTOXIN BMK M8


Theoretical massNumber of molelcules
Total (without water)6,9551
Polymers6,9551
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.320, 38.560, 29.150
Angle α, β, γ (deg.)90.00, 107.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NEUROTOXIN BMK M8 / SCORPION NEUROTOXIN BMK M8 / TOXIN BMK-VIII


Mass: 6954.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mesobuthus martensii (Chinese scorpion) / Organ: TAIL / References: UniProt: P54135
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.81 Å3/Da / Density % sol: 33 %
Crystal grow
*PLUS
pH: 4.55 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.02 M1dropHCl
30.2 M1dropNaH2PO4

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 14, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.85 Å / Num. obs: 3802 / % possible obs: 88.4 % / Redundancy: 1.6 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.0523 / Net I/σ(I): 10.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 1.15 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 4.59 / % possible all: 17.3
Reflection
*PLUS
Num. measured all: 6130

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Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AAH II

Resolution: 1.9→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.181 --
obs0.181 3615 92.4 %
Displacement parametersBiso mean: 16.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms482 0 0 141 623
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_deg2.175
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.04
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.2
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: 1.9→1.97 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.273 246 -
obs--62.4 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.04
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.2

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