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- PDB-3e8y: Xray structure of scorpion toxin BmBKTx1 -

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Basic information

Entry
Database: PDB / ID: 3e8y
TitleXray structure of scorpion toxin BmBKTx1
ComponentsPotassium channel toxin alpha-KTx 19.1
KeywordsTOXIN / racemic protein / direct methods / Xray crystal stucture / Ionic channel inhibitor / Neurotoxin / Potassium channel inhibitor / Secreted
Function / homologyScorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 19.1
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å
AuthorsMandal, K. / Pentelute, B.L. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: X-ray structure of native scorpion toxin BmBKTx1 by racemic protein crystallography using direct methods.
Authors: Mandal, K. / Pentelute, B.L. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B.
History
DepositionAug 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
X: Potassium channel toxin alpha-KTx 19.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4803
Polymers3,3481
Non-polymers1322
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.633, 56.633, 31.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number88
Space group name H-MI41/a
Components on special symmetry positions
IDModelComponents
11X-101-

CL

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Components

#1: Protein/peptide Potassium channel toxin alpha-KTx 19.1 / Neurotoxin BmBKTx1 / BmK37


Mass: 3348.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical synthesis / References: UniProt: P83407
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1 M citric acid, 2 M ammonium sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97911 Å
DetectorType: MAR CCD 300 / Detector: CCD / Date: Aug 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 17925 / % possible obs: 99.78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 41.6
Reflection shellResolution: 1.1→1.129 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2.35 / % possible all: 97.33

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.453 / SU ML: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / 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
Rfree0.21737 2035 10.2 %RANDOM
Rwork0.20006 ---
obs0.20175 17925 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.096 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms240 0 6 22 268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022255
X-RAY DIFFRACTIONr_angle_refined_deg1.921.996348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.074541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.906245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9661555
X-RAY DIFFRACTIONr_chiral_restr0.1240.237
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02175
X-RAY DIFFRACTIONr_nbd_refined0.2110.291
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.25
X-RAY DIFFRACTIONr_mcbond_it2.2441.5174
X-RAY DIFFRACTIONr_mcangle_it3.2152270
X-RAY DIFFRACTIONr_scbond_it4.556396
X-RAY DIFFRACTIONr_scangle_it5.3354.572
X-RAY DIFFRACTIONr_rigid_bond_restr2.2973270
X-RAY DIFFRACTIONr_sphericity_free10.207323
X-RAY DIFFRACTIONr_sphericity_bonded5.9283245
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 149 -
Rwork0.27 1275 -
obs--97.33 %

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