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Basic information

Entry
Database: PDB / ID: 6atn
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsPotassium channel toxin alpha-KTx 4.5
KeywordsTOXIN / Knottins / Cystine knot / Toxins
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 4.5
Function and homology information
Biological speciesTityus costatus (scorpion)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.76 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 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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 alpha-KTx 4.5


Theoretical massNumber of molelcules
Total (without water)4,1441
Polymers4,1441
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.567, 46.567, 44.337
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsMonomer as determined by gel filtration.

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Components

#1: Protein/peptide Potassium channel toxin alpha-KTx 4.5


Mass: 4144.028 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tityus costatus (scorpion) / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: Q5G8B6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.9 Å3/Da / Density % sol: 57.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M Na malonate pH 7.0

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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: Apr 4, 2016
RadiationMonochromator: osmic varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 8524 / % possible obs: 44.7 % / Redundancy: 2.1 % / Χ2: 2.1 / Net I/σ(I): 25.05
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.159 / Num. unique obs: 62 / CC1/2: 0.94 / Rpim(I) all: 0.173 / % possible all: 6.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→32.93 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.829 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22607 236 5.1 %RANDOM
Rwork0.16866 ---
obs0.17157 4375 89.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.843 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.76→32.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms283 0 0 45 328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019290
X-RAY DIFFRACTIONr_bond_other_d0.0010.02289
X-RAY DIFFRACTIONr_angle_refined_deg1.4522.022386
X-RAY DIFFRACTIONr_angle_other_deg0.8133680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.969538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.97724.2867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5841559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.28151
X-RAY DIFFRACTIONr_chiral_restr0.1240.239
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021313
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0252
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_it1.9571.394155
X-RAY DIFFRACTIONr_mcbond_other1.9051.388154
X-RAY DIFFRACTIONr_mcangle_it2.8773.109192
X-RAY DIFFRACTIONr_mcangle_other2.8893.116193
X-RAY DIFFRACTIONr_scbond_it4.571.866135
X-RAY DIFFRACTIONr_scbond_other4.571.864135
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4853.876194
X-RAY DIFFRACTIONr_long_range_B_refined8.86927.817315
X-RAY DIFFRACTIONr_long_range_B_other8.85927.25309
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.764→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 5 -
Rwork0.264 99 -
obs--28.18 %

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