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- PDB-1seg: Crystal structure of a toxin chimera between Lqh-alpha-IT from th... -

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Basic information

Entry
Database: PDB / ID: 1seg
TitleCrystal structure of a toxin chimera between Lqh-alpha-IT from the scorpion Leiurus quinquestriatus hebraeus and AAH2 from Androctonus australis hector
ComponentsAAH2: LQH-ALPHA-IT (FACE) CHIMERIC TOXIN
KeywordsTOXIN / CHIMERA / 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
NITRATE ION / PROPANOIC ACID / Alpha-mammal toxin AaH2
Similarity search - Component
Biological speciesAndroctonus australis hector (scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.3 Å
AuthorsKarbat, I. / Frolow, F. / Froy, O. / Gilles, N. / Cohen, L. / Turkov, M. / Gordon, D. / Gurevitz, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Molecular basis of the high insecticidal potency of scorpion alpha-toxins.
Authors: Karbat, I. / Frolow, F. / Froy, O. / Gilles, N. / Cohen, L. / Turkov, M. / Gordon, D. / Gurevitz, M.
History
DepositionFeb 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 30, 2014Group: Data collection
Revision 1.4Oct 27, 2021Group: 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 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Residues 8-10, 17, 56-59, 62 of Lqh-alpha-IT constructed on the scaffold of AAH2: D8K, ...SEQUENCE Residues 8-10, 17, 56-59, 62 of Lqh-alpha-IT constructed on the scaffold of AAH2: D8K, D9N, V10Y, G17F, R56P, T57I, K58R, G59V, R62K

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AAH2: LQH-ALPHA-IT (FACE) CHIMERIC TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7185
Polymers7,4231
Non-polymers2944
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.523, 74.523, 56.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-182-

HOH

21A-205-

HOH

31A-287-

HOH

DetailsThe molecule is biologically active as a monomer

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Components

#1: Protein AAH2: LQH-ALPHA-IT (FACE) CHIMERIC TOXIN / AaH II / AaHII / AaH2


Mass: 7423.493 Da / Num. of mol.: 1
Mutation: D8K, D9N, V10Y, G17F, R56P, T57I, K58R, G59V, R62K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Androctonus australis hector (scorpion)
Species: Androctonus australis / Strain: hector / Plasmid: pET-11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01484
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.64 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM trisodium citrate dihydrate, 1M mono-ammonium dihydrogen phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.003 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 1.3→52.7 Å / Num. obs: 19554 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 14.115 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 25.9
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 12 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 5.1 / Num. unique all: 19647 / Rsym value: 0.051 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1AHO

1aho


Resolution: 1.3→52.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.916 / SU ML: 0.037
Isotropic thermal model: ANISOTROPIC TEMPERATURE FACTORS REFINED
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17802 1002 5.1 %RANDOM
Rwork0.15349 ---
all0.15472 ---
obs0.15472 18549 97.57 %-
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: 14.787 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å20 Å20 Å2
2---1.96 Å20 Å2
3---3.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.047 Å0.047 Å
Refinement stepCycle: LAST / Resolution: 1.3→52.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms518 0 18 119 655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021553
X-RAY DIFFRACTIONr_bond_other_d0.0020.02436
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.968748
X-RAY DIFFRACTIONr_angle_other_deg0.84431027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.483563
X-RAY DIFFRACTIONr_chiral_restr0.1090.269
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02615
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02118
X-RAY DIFFRACTIONr_nbd_refined0.220.2116
X-RAY DIFFRACTIONr_nbd_other0.2490.2516
X-RAY DIFFRACTIONr_nbtor_other0.0820.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0610.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1570.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.222
X-RAY DIFFRACTIONr_mcbond_it1.5741.5325
X-RAY DIFFRACTIONr_mcangle_it2.1762512
X-RAY DIFFRACTIONr_scbond_it3.3483228
X-RAY DIFFRACTIONr_scangle_it4.7634.5236
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.222 53
Rwork0.227 1251
obs-1251
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42730.0683-0.36721.0158-0.20780.23-0.0218-0.0097-0.0131-0.0647-0.0346-0.13940.01430.02020.05640.04820.00180.01220.05890.01160.006318.28375.47718.639
249.1963-14.7472-5.47938.4477-11.5192-10.2743-0.0056-0.219-0.2385-0.34630.4597-0.18250.07050.0273-0.4540.0553-0.00770.00260.06020.00640.000912.99684.31219.175
32.987835.091110.5432-2.4731-0.7724-6.69560.0017-1.16141.32440.7026-0.10120.5419-1.543-0.66940.09950.0382-0.00130.00020.03820.00150.039419.35193.22921.649
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 641 - 64
2X-RAY DIFFRACTION2AB1651
3X-RAY DIFFRACTION3AC1661

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