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- PDB-1chz: A NEW NEUROTOXIN FROM BUTHUS MARTENSII KARSCH -

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Basic information

Entry
Database: PDB / ID: 1chz
TitleA NEW NEUROTOXIN FROM BUTHUS MARTENSII KARSCH
ComponentsPROTEIN (BMK M2)
KeywordsTOXIN / NEUROTOXIN / 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
Alpha-like toxin BmK M2
Similarity search - Component
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsHe, X.L. / Deng, J.P. / Li, H.M. / Wang, D.C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of a new neurotoxin from the scorpion Buthus martensii Karsch at 1.76 A.
Authors: He, X.L. / Deng, J.P. / Wang, M. / Zhang, Y. / 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: Zool.Res.Sinica. / Year: 1989
Title: Purification and Partial Characterization of Several New Nerotoxins from East- Asia Scorpion
Authors: Hu, R.Q. / Wang, M. / Liu, J.N. / Lei, K.J.
History
DepositionMar 31, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2014Group: Database references
Revision 1.4Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (BMK M2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2582
Polymers7,2221
Non-polymers351
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.640, 37.310, 37.950
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 PROTEIN (BMK M2)


Mass: 7222.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mesobuthus martensii (Chinese scorpion) / Organ: TAIL / Tissue: GLAND / References: UniProt: P58488
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.83 Å3/Da / Density % sol: 31.51 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMacetate1drop
210 mg/mlprotein1drop
365-70 %MPD1reservoir
40.1 MTris1reservoir
55 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→20 Å / Num. obs: 5004 / % possible obs: 90 % / Redundancy: 2.4 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.1
Reflection shellResolution: 1.76→1.82 Å / % possible all: 55.3
Reflection
*PLUS
% possible obs: 90 % / Num. measured all: 11634 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 55.3 % / Rmerge(I) obs: 0.34

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SNB

1snb


Resolution: 1.76→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 1.0E-5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 -10 %RANDOM
Rwork0.19 ---
obs-4938 90 %-
Displacement parametersBiso mean: 23 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.76→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms502 0 1 87 590
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.902
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.85
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.175
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: 1.76→1.82 Å / Total num. of bins used: 10 /
Rfactor% reflection
Rfree0.364 10 %
Rwork0.3 -
obs-55.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.85
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.175
LS refinement shell
*PLUS
Rfactor Rfree: 0.364 / % reflection Rfree: 10 % / Rfactor Rwork: 0.3

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