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Basic information

Entry
Database: PDB / ID: 6aup
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsPotassium channel toxin gamma-KTx 2.2
KeywordsTOXIN / Knottins / Cystine knot / Toxins
Function / homologyScorpion 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 gamma-KTx 2.2
Function and homology information
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionSep 1, 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 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium channel toxin gamma-KTx 2.2
B: Potassium channel toxin gamma-KTx 2.2
C: Potassium channel toxin gamma-KTx 2.2
F: Potassium channel toxin gamma-KTx 2.2
D: Potassium channel toxin gamma-KTx 2.2
E: Potassium channel toxin gamma-KTx 2.2
G: Potassium channel toxin gamma-KTx 2.2
H: Potassium channel toxin gamma-KTx 2.2
I: Potassium channel toxin gamma-KTx 2.2
J: Potassium channel toxin gamma-KTx 2.2
K: Potassium channel toxin gamma-KTx 2.2
L: Potassium channel toxin gamma-KTx 2.2
M: Potassium channel toxin gamma-KTx 2.2
N: Potassium channel toxin gamma-KTx 2.2
O: Potassium channel toxin gamma-KTx 2.2
P: Potassium channel toxin gamma-KTx 2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,06343
Polymers66,49316
Non-polymers2,57027
Water4,035224
1
A: Potassium channel toxin gamma-KTx 2.2
B: Potassium channel toxin gamma-KTx 2.2
C: Potassium channel toxin gamma-KTx 2.2
F: Potassium channel toxin gamma-KTx 2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,29211
Polymers16,6234
Non-polymers6687
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-101 kcal/mol
Surface area7440 Å2
MethodPISA
2
D: Potassium channel toxin gamma-KTx 2.2
E: Potassium channel toxin gamma-KTx 2.2
G: Potassium channel toxin gamma-KTx 2.2
H: Potassium channel toxin gamma-KTx 2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,48013
Polymers16,6234
Non-polymers8579
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-101 kcal/mol
Surface area7380 Å2
MethodPISA
3
I: Potassium channel toxin gamma-KTx 2.2
J: Potassium channel toxin gamma-KTx 2.2
K: Potassium channel toxin gamma-KTx 2.2
L: Potassium channel toxin gamma-KTx 2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0969
Polymers16,6234
Non-polymers4725
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-75 kcal/mol
Surface area7360 Å2
MethodPISA
4
M: Potassium channel toxin gamma-KTx 2.2
N: Potassium channel toxin gamma-KTx 2.2
O: Potassium channel toxin gamma-KTx 2.2
P: Potassium channel toxin gamma-KTx 2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,19610
Polymers16,6234
Non-polymers5726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-93 kcal/mol
Surface area7650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.878, 80.444, 94.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
Potassium channel toxin gamma-KTx 2.2 / BmKK7 / BmKKx2


Mass: 4155.808 Da / Num. of mol.: 16 / Fragment: residues 22-57
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesobuthus martensii (Chinese scorpion)
Cell (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P59938
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 1.68 Å3/Da / Density % sol: 26.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 100 mM sodium acetate pH 4.6, 2 M (NH4)2SO4

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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: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→61.17 Å / Num. obs: 32452 / % possible obs: 98 % / Redundancy: 48.3 % / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.023 / Χ2: 2.446 / Net I/σ(I): 46.8
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 23.7 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 8.5 / Num. unique obs: 2732 / CC1/2: 0.962 / Rpim(I) all: 0.13 / Χ2: 2.312 / % possible all: 80

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J5J

1j5j


Resolution: 1.95→61.17 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.75 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22492 1620 5 %RANDOM
Rwork0.17313 ---
obs0.17577 30946 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.95→61.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 141 224 4917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194806
X-RAY DIFFRACTIONr_bond_other_d0.0010.024152
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9856470
X-RAY DIFFRACTIONr_angle_other_deg0.80339695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1675596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.07121.875192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31415768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0151546
X-RAY DIFFRACTIONr_chiral_restr0.0990.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215276
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021050
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_it1.7091.8862420
X-RAY DIFFRACTIONr_mcbond_other1.7091.8852419
X-RAY DIFFRACTIONr_mcangle_it2.4073.1472998
X-RAY DIFFRACTIONr_mcangle_other2.4083.1472999
X-RAY DIFFRACTIONr_scbond_it3.192.4932386
X-RAY DIFFRACTIONr_scbond_other3.1792.4922386
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6263.9643471
X-RAY DIFFRACTIONr_long_range_B_refined6.03517.955016
X-RAY DIFFRACTIONr_long_range_B_other6.03317.9465016
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 101 -
Rwork0.185 1882 -
obs--81.94 %

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