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Basic information

Entry
Database: PDB / ID: 6ats
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsPotassium channel toxin kappa-KTx 1.2
KeywordsTOXIN / Knottins / Cystine knot / Toxins
Function / homologyHefutoxin / Hefutoxin family / defense response to fungus / potassium channel regulator activity / toxin activity / killing of cells of another organism / extracellular region / Potassium channel toxin kappa-KTx 1.2
Function and homology information
Biological speciesHeterometrus fulvipes (Indian black scorpion)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.9 Å
AuthorsGewe, M.M. / Rupert, P. / Strong, R.K.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Screening, large-scale production and structure-based classification of cystine-dense peptides.
Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S. ...Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S.M. / May, D. / Watson, A. / Chan, M.K. / Bahl, C.D. / Olson, J.M. / Strong, R.K.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Oct 23, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel toxin kappa-KTx 1.2


Theoretical massNumber of molelcules
Total (without water)2,8661
Polymers2,8661
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.102, 21.323, 20.368
Angle α, β, γ (deg.)90.00, 92.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Potassium channel toxin kappa-KTx 1.2 / Kappa-hefutoxin-2 / Kappa-HfTx2


Mass: 2866.093 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heterometrus fulvipes (Indian black scorpion)
Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P82851
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1.78 Å3/Da / Density % sol: 30.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 20% Ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 2535 / % possible obs: 89.6 % / Redundancy: 2.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.022 / Χ2: 1.506 / Net I/σ(I): 14.45
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.035 / Num. unique obs: 63 / CC1/2: 0.994 / Rpim(I) all: 0.028 / % possible all: 45

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→23.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.592 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17907 55 3.9 %RANDOM
Rwork0.13207 ---
obs0.13412 1370 87.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.05 Å2
2--0.01 Å20 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.9→23.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms193 0 0 32 225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019207
X-RAY DIFFRACTIONr_bond_other_d0.0020.02166
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.902278
X-RAY DIFFRACTIONr_angle_other_deg0.9253386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.273525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.83422.14314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6611536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.094154
X-RAY DIFFRACTIONr_chiral_restr0.1130.223
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0252
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_it1.2571.62297
X-RAY DIFFRACTIONr_mcbond_other1.2231.6296
X-RAY DIFFRACTIONr_mcangle_it1.762.741120
X-RAY DIFFRACTIONr_mcangle_other1.7622.741121
X-RAY DIFFRACTIONr_scbond_it3.9042.32110
X-RAY DIFFRACTIONr_scbond_other3.9222.325109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6243.664157
X-RAY DIFFRACTIONr_long_range_B_refined5.99416.29258
X-RAY DIFFRACTIONr_long_range_B_other5.91515.78253
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 6 -
Rwork0.177 51 -
obs--46.34 %

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