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- PDB-2i61: Depressant anti-insect neurotoxin, LqhIT2 from Leiurus quinquestr... -

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Basic information

Entry
Database: PDB / ID: 2i61
TitleDepressant anti-insect neurotoxin, LqhIT2 from Leiurus quinquestriatus hebraeus
ComponentsInsect toxin 2
KeywordsTOXIN / Scorpion toxin / depressant / anti-insect / sodium channel modifer
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
ACETIC ACID / CARBON DIOXIDE / : / Beta-insect depressant toxin LqhIT2
Similarity search - Component
Biological speciesLeiurus quinquestriatus hebraeus (scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFrolow, F. / Gurevitz, M. / Karbat, I. / Turkov, M. / Gordon, D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: X-ray Structure and Mutagenesis of the Scorpion Depressant Toxin LqhIT2 Reveals Key Determinants Crucial for Activity and Anti-Insect Selectivity.
Authors: Karbat, I. / Turkov, M. / Cohen, L. / Kahn, R. / Gordon, D. / Gurevitz, M. / Frolow, F.
History
DepositionAug 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insect toxin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,31310
Polymers6,9061
Non-polymers4079
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)19.660, 51.423, 28.917
Angle α, β, γ (deg.)90.00, 107.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Insect toxin 2 / / Lqh IT2 / LqhIT2 / LqhIT2-44 / anti-insect depressant neurotoxin


Mass: 6905.811 Da / Num. of mol.: 1 / Fragment: Peptide modifier of voltage-gated sodium channels
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leiurus quinquestriatus hebraeus (scorpion)
Species: Leiurus quinquestriatus / Strain: hebraeus / Plasmid: pET11c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q26292

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Non-polymers , 6 types, 95 molecules

#2: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Li
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#6: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


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


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein concentration 8mg/ml, precepitant 1.5 M LiSO4, buffer 0.1 M NA, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0052 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2002 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0052 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 16312 / Num. obs: 16312 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 6.81 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Χ2: 2.619 / Net I/σ(I): 43.63
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.046 / Mean I/σ(I) obs: 22.77 / Num. unique all: 773 / Rsym value: 0.046 / Χ2: 1.512 / % possible all: 90.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation4 Å27.54 Å
Translation4 Å27.54 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ProDCdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2SN3

2sn3


Resolution: 1.2→27.54 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.659 / SU ML: 0.014 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.03 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12 830 5.1 %RANDOM
Rwork0.096 ---
all0.097 16312 --
obs0.097 16246 94.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.216 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.1 Å2
2--0.56 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.2→27.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms501 0 27 90 618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021543
X-RAY DIFFRACTIONr_bond_other_d0.0020.02390
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.965728
X-RAY DIFFRACTIONr_angle_other_deg0.9273.017932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.479567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.91124.09122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9161590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.314152
X-RAY DIFFRACTIONr_chiral_restr0.1210.266
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02111
X-RAY DIFFRACTIONr_nbd_refined0.2620.2110
X-RAY DIFFRACTIONr_nbd_other0.1940.2383
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2256
X-RAY DIFFRACTIONr_nbtor_other0.0860.2296
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.248
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.218
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.110.23
X-RAY DIFFRACTIONr_mcbond_it3.3873415
X-RAY DIFFRACTIONr_mcbond_other1.5263138
X-RAY DIFFRACTIONr_mcangle_it3.7415497
X-RAY DIFFRACTIONr_scbond_it5.6427291
X-RAY DIFFRACTIONr_scangle_it6.55510227
X-RAY DIFFRACTIONr_rigid_bond_restr2.61131244
X-RAY DIFFRACTIONr_sphericity_free13.164389
X-RAY DIFFRACTIONr_sphericity_bonded5.063919
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.098 60 -
Rwork0.067 1090 -
obs-1150 90.84 %

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