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- PDB-4hhf: Crystal Structure of chemically synthesized scorpion alpha-toxin OD1 -

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Basic information

Entry
Database: PDB / ID: 4hhf
TitleCrystal Structure of chemically synthesized scorpion alpha-toxin OD1
ComponentsAlpha-toxin OD1
KeywordsTOXIN / scorpion long-chain alpha-toxin / gating modulator / voltage-gated sodium channels 1.4 / 1.6 / 1.7 / inhibition of fast channel inactivation / C-terminally amidated / venom gland
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
Biological speciesOdontobuthus doriae (scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, C.I.A. / Lewis, R.J. / Alewood, P.F. / Durek, T.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Chemical engineering and structural and pharmacological characterization of the alpha-scorpion toxin OD1.
Authors: Durek, T. / Vetter, I. / Wang, C.I. / Motin, L. / Knapp, O. / Adams, D.J. / Lewis, R.J. / Alewood, P.F.
History
DepositionOct 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-toxin OD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5764
Polymers7,2211
Non-polymers3553
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)48.727, 48.727, 63.245
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Alpha-toxin OD1


Mass: 7221.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Odontobuthus doriae (scorpion) / References: UniProt: P84646
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 uL 20 mg/mL lyophilized toxin in 2 mM hydrochloric acid + 1 uL reservoir (0.1 M Tris-HCl, pH 7.5, 2% v/v dioxane, 56-60% v/v MPD) against 500 uL reservoir (rod-shaped crystals appeared ...Details: 1 uL 20 mg/mL lyophilized toxin in 2 mM hydrochloric acid + 1 uL reservoir (0.1 M Tris-HCl, pH 7.5, 2% v/v dioxane, 56-60% v/v MPD) against 500 uL reservoir (rod-shaped crystals appeared after 24 hours, grew to 0.5 x 0.1 x 0.1 mm), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.58→35.1 Å / Num. all: 8454 / Num. obs: 8431 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.21 % / Biso Wilson estimate: 11.76 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 22.1
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 1.54 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 1.5 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.6.0117refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SN1
Resolution: 1.8→35.1 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.775 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.11 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20192 397 4.9 %RANDOM
Rwork0.18511 ---
obs0.18593 7763 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.213 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms501 0 24 45 570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.02536
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6711.978730
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.504564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39523.7524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2151580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.025154
X-RAY DIFFRACTIONr_chiral_restr0.2980.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021400
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 23 -
Rwork0.251 469 -
obs--86.77 %
Refinement TLS params.Method: refined / Origin x: 4.6911 Å / Origin y: 28.7693 Å / Origin z: 8.0233 Å
111213212223313233
T0.0185 Å20.0056 Å2-0.0013 Å2-0.0072 Å2-0.0054 Å2--0.0286 Å2
L0.1918 °2-0.3032 °2-0.1937 °2-0.5239 °20.2118 °2--0.4901 °2
S-0.0127 Å °0.0185 Å °-0.0041 Å °0.028 Å °-0.022 Å °-0.0221 Å °-0.0022 Å °-0.0254 Å °0.0347 Å °

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