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- PDB-1t0z: Structure of an Excitatory Insect-specific Toxin with an Analgesi... -

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Basic information

Entry
Database: PDB / ID: 1t0z
TitleStructure of an Excitatory Insect-specific Toxin with an Analgesic Effect on Mammalian from Scorpion Buthus martensii Karsch
Componentsinsect neurotoxin
KeywordsTOXIN / alpha-beta
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 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
Beta-insect excitatory toxin BmK IT-AP
Similarity search - Component
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, C. / Guan, R.-J. / Xiang, Y. / Zhang, Y. / Wang, D.-C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of an excitatory insect-specific toxin with an analgesic effect on mammals from the scorpion Buthus martensii Karsch.
Authors: Li, C. / Guan, R.J. / Xiang, Y. / Zhang, Y. / Wang, D.C.
#1: Journal: Toxicon / Year: 1999
Title: Molecular characterization of a new excitatory insect neurotoxin with an analgesic effect on mice from the scorpion Buthus martensii Karsch
Authors: Xiong, Y.-M. / Lan, Z.-D. / Wang, M. / Liu, B. / Liu, X.-Q. / Fei, H. / Xu, L.-G. / Xia, Q.-C. / Wang, C.-G. / Wang, D.-C. / Chi, Z.-W.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray analyses of insect neurotoxins with analgesic effect from the scorpion Buthus martensii Karsch
Authors: Guan, R.-J. / Liu, X.-Q. / Liu, B. / Wang, M. / Wang, D.-C.
History
DepositionApr 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: insect neurotoxin
B: insect neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,38713
Polymers16,3312
Non-polymers1,05711
Water1,18966
1
A: insect neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9349
Polymers8,1651
Non-polymers7698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: insect neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4534
Polymers8,1651
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: insect neurotoxin
B: insect neurotoxin
hetero molecules

A: insect neurotoxin
B: insect neurotoxin
hetero molecules

A: insect neurotoxin
B: insect neurotoxin
hetero molecules

A: insect neurotoxin
B: insect neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,54952
Polymers65,3228
Non-polymers4,22744
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area14660 Å2
ΔGint-742 kcal/mol
Surface area32290 Å2
MethodPISA
4
A: insect neurotoxin
hetero molecules

A: insect neurotoxin
hetero molecules

B: insect neurotoxin
hetero molecules

B: insect neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,77426
Polymers32,6614
Non-polymers2,11322
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area5850 Å2
ΔGint-359 kcal/mol
Surface area17630 Å2
MethodPISA
5
A: insect neurotoxin
hetero molecules

A: insect neurotoxin
hetero molecules

B: insect neurotoxin
hetero molecules

B: insect neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,77426
Polymers32,6614
Non-polymers2,11322
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+2/31
crystal symmetry operation5_565y,-x+y+1,z+1/31
crystal symmetry operation7_555y,x,-z+1/31
Buried area6280 Å2
ΔGint-367 kcal/mol
Surface area17190 Å2
MethodPISA
6
A: insect neurotoxin
hetero molecules

A: insect neurotoxin
hetero molecules

B: insect neurotoxin
hetero molecules

B: insect neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,77426
Polymers32,6614
Non-polymers2,11322
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+2/31
crystal symmetry operation2_665-y+1,x-y+1,z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area5640 Å2
ΔGint-330 kcal/mol
Surface area17830 Å2
MethodPISA
7
A: insect neurotoxin
B: insect neurotoxin
hetero molecules

A: insect neurotoxin
B: insect neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,77426
Polymers32,6614
Non-polymers2,11322
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area6530 Å2
ΔGint-360 kcal/mol
Surface area16950 Å2
MethodPISA
8
A: insect neurotoxin
hetero molecules

B: insect neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,38713
Polymers16,3312
Non-polymers1,05711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area2590 Å2
ΔGint-173 kcal/mol
Surface area9150 Å2
MethodPISA
9
A: insect neurotoxin
hetero molecules

A: insect neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,86818
Polymers16,3312
Non-polymers1,53716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+2/31
Buried area3660 Å2
ΔGint-219 kcal/mol
Surface area8590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.971, 64.971, 173.482
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-143-

HOH

21A-148-

HOH

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Components

#1: Protein insect neurotoxin


Mass: 8165.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mesobuthus martensii (Chinese scorpion) / References: UniProt: O77091
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.24 Å3/Da / Density % sol: 61.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulfate, Dioxane, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→500 Å / Num. obs: 7244 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 41.7 Å2
Reflection shellResolution: 2.6→2.76 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.53 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 102842.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 763 10.9 %RANDOM
Rwork0.2 ---
obs-7027 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.3929 Å2 / ksol: 0.360574 e/Å3
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å22.19 Å20 Å2
2--0.42 Å20 Å2
3----0.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 55 66 1257
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 112 10.6 %
Rwork0.242 942 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMINP.TOP

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