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- PDB-1sn4: STRUCTURE OF SCORPION NEUROTOXIN BMK M4 -

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Basic information

Entry
Database: PDB / ID: 1sn4
TitleSTRUCTURE OF SCORPION NEUROTOXIN BMK M4
ComponentsPROTEIN (NEUROTOXIN BMK M4)
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
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
ACETATE ION / Neurotoxin BmK-M9 / Alpha-like toxin BmK-M4
Similarity search - Component
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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: 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: Zool.Res.Sinica. / Year: 1989
Title: Purification and Partial Characterization of Several New Neurotoxins from East_ Asia Scorpion Crystallographic Studies on an Acidic Toxin from Scorpion Buthus Martensii Karsch
Authors: Hu, R.Q. / Wang, M. / LIU, J.N. / LEI, K.J.
#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: Toxicon / Year: 1997
Title: Purification and Sequence Determination of a New Neutral Mammalian Neurotoxin from the Scorpion Buthus Martensii Karsch
Authors: Luo, M.J. / Xiong, Y.M. / Wang, M. / Wang, D.C. / Chi, C.W.
#5: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal Structure of an Acidic Neurotoxin from Scorpion Buthus Martensii Karsch at 1.85A Resolution
Authors: Li, H.M. / Wang, D.C. / Jin, L. / ZENG, Z.H. / Hu, R.Q.
History
DepositionNov 11, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (NEUROTOXIN BMK M4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3256
Polymers7,0301
Non-polymers2955
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.880, 54.880, 33.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PROTEIN (NEUROTOXIN BMK M4) / BMK-IV


Mass: 7029.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mesobuthus martensii (Chinese scorpion) / Organ: TAIL / Secretion: VENOM / References: UniProt: P45698, UniProt: P58328*PLUS
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.001 Macetic acid1drop
34.8 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: Dec 14, 1991
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→21.3 Å / Num. obs: 10577 / % possible obs: 73.5 % / Redundancy: 2.2 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 3.7
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / % possible all: 51.2
Reflection
*PLUS
Num. obs: 10578 / Num. measured all: 23268
Reflection shell
*PLUS
% possible obs: 60.2 %

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Processing

Software
NameClassification
WEISdata scaling
WEISdata reduction
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BMK M1

Resolution: 1.3→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.192 998 10 %RANDOM
Rwork0.166 ---
obs0.166 10577 73.5 %-
Displacement parametersBiso mean: 26.9 Å2
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms492 0 20 117 629
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_deg1.732
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.38
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.065
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: 1.3→1.35 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.343 72 10.8 %
Rwork0.299 662 -
obs--51.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.38
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.065
LS refinement shell
*PLUS
Rfactor Rfree: 0.343 / % reflection Rfree: 10.8 % / Rfactor Rwork: 0.299

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