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- PDB-1omy: Crystal Structure of a Recombinant alpha-insect Toxin BmKaIT1 fro... -

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Basic information

Entry
Database: PDB / ID: 1omy
TitleCrystal Structure of a Recombinant alpha-insect Toxin BmKaIT1 from the scorpion Buthus martensii Karsch
ComponentsAlpha-neurotoxin TX12
KeywordsTOXIN / alpha-insect toxin / sodium channel
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
ACETIC ACID / Toxin BmKaIT1
Similarity search - Component
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHuang, Y. / Huang, Q. / Chen, H. / Tang, Y. / Miyake, H. / Kusunoki, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary crystallographic study of rBmKalphaIT1, a recombinant alpha-insect toxin from the scorpion Buthus martensii Karsch.
Authors: Huang, Y. / Huang, Q. / Chen, H. / Tang, Y. / Miyake, H. / Kusunoki, M.
History
DepositionFeb 26, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: 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 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-neurotoxin TX12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4263
Polymers7,3301
Non-polymers962
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.241, 36.507, 57.080
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 Alpha-neurotoxin TX12 / rBmKaIT1


Mass: 7330.416 Da / Num. of mol.: 1 / Fragment: residues 2-65
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesobuthus martensii (Chinese scorpion)
Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9GQW3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.08 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 296 K / pH: 5.9
Details: Na2HPO4, VAPOR DIFFUSION, HANGING DROP, pH 5.90, temperature 296.0K
Crystal grow
*PLUS
Temperature: 296 K / pH: 4.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMacetic acid1drop
30.02 %(w/v)1droppH4.2NaN3
41.0 M1reservoirNa2HPO4
50.02 %(w/v)1reservoirNaN3
65.0 %(v/v)dioxane1reservoirpH5.9

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→26.72 Å / Num. obs: 4614 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 4.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.11 Å / Num. obs: 3971 / Num. measured all: 26193 / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 6.5 % / Num. unique obs: 622 / Num. measured obs: 4044 / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
DPSdata collection
DPSdata reduction
CNSrefinement
MOSFLMdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SN1

1sn1


Resolution: 2→26.72 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.218 480 10.4 %RANDOM
Rwork0.185 ---
obs0.185 4590 99.9 %-
all-4615 --
Refinement stepCycle: LAST / Resolution: 2→26.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms499 0 1 42 542
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00469
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.24094
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.11 Å / Total num. of bins used: 10 / % reflection obs: 99.9 %
Refinement
*PLUS
Highest resolution: 2.11 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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