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- PDB-4z7p: X-ray structure of racemic ShK Q16K toxin -

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Basic information

Entry
Database: PDB / ID: 4z7p
TitleX-ray structure of racemic ShK Q16K toxin
ComponentsPotassium channel toxin kappa-stichotoxin-She1a
KeywordsTOXIN / ShK toxin
Function / homologyShKT domain / ShKT domain profile. / nematocyst / potassium channel regulator activity / toxin activity / defense response to bacterium / extracellular region / Kappa-stichotoxin-She3a
Function and homology information
Biological speciesStoichactis helianthus (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsSickmier, E.A.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Pharmaceutical Optimization of Peptide Toxins for Ion Channel Targets: Potent, Selective, and Long-Lived Antagonists of Kv1.3.
Authors: Murray, J.K. / Qian, Y.X. / Liu, B. / Elliott, R. / Aral, J. / Park, C. / Zhang, X. / Stenkilsson, M. / Salyers, K. / Rose, M. / Li, H. / Yu, S. / Andrews, K.L. / Colombero, A. / Werner, J. ...Authors: Murray, J.K. / Qian, Y.X. / Liu, B. / Elliott, R. / Aral, J. / Park, C. / Zhang, X. / Stenkilsson, M. / Salyers, K. / Rose, M. / Li, H. / Yu, S. / Andrews, K.L. / Colombero, A. / Werner, J. / Gaida, K. / Sickmier, E.A. / Miu, P. / Itano, A. / McGivern, J. / Gegg, C.V. / Sullivan, J.K. / Miranda, L.P.
History
DepositionApr 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Nov 6, 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 / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel toxin kappa-stichotoxin-She1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5516
Polymers4,0711
Non-polymers4805
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.783, 60.783, 43.592
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number148
Space group name H-MH-3
Components on special symmetry positions
IDModelComponents
11A-102-

SO4

21A-102-

SO4

31A-232-

HOH

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Components

#1: Protein/peptide Potassium channel toxin kappa-stichotoxin-She1a / kappa-SHTX-She1a / Potassium channel toxin ShK


Mass: 4070.943 Da / Num. of mol.: 1 / Mutation: Q16K / Source method: obtained synthetically / Source: (synth.) Stoichactis helianthus (sea anemone) / References: UniProt: P29187
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 35.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.5, 2-2.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 18716 / % possible obs: 99.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.061 / Χ2: 1.013 / Net I/av σ(I): 22.419 / Net I/σ(I): 10 / Num. measured all: 98807
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.2-1.243.50.617681.03594.2
1.24-1.294.60.47318820.99699.6
1.29-1.355.30.40419031.037100
1.35-1.425.50.28718881.086100
1.42-1.515.60.20618621.082100
1.51-1.635.60.12418771.034100
1.63-1.795.60.09618840.984100
1.79-2.055.60.07518830.947100
2.05-2.595.60.05318801.008100
2.59-505.70.03818890.938100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→30.39 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.2443 / WRfactor Rwork: 0.2219 / FOM work R set: 0.8758 / SU B: 0.962 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0399 / SU Rfree: 0.0401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 914 5.1 %RANDOM
Rwork0.204 ---
obs0.2051 17078 95.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.25 Å2 / Biso mean: 16.774 Å2 / Biso min: 7.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.16 Å2-0 Å2
2--0.16 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 1.2→30.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms278 0 24 38 340
Biso mean--26.8 30.51 -
Num. residues----35
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.019313
X-RAY DIFFRACTIONr_bond_other_d0.0010.02296
X-RAY DIFFRACTIONr_angle_refined_deg1.0382.036419
X-RAY DIFFRACTIONr_angle_other_deg0.7423.018678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.1871610
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.0221563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.111155
X-RAY DIFFRACTIONr_chiral_restr0.0610.246
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0272
X-RAY DIFFRACTIONr_mcbond_it1.0381.838141
X-RAY DIFFRACTIONr_mcbond_other1.021.836140
X-RAY DIFFRACTIONr_mcangle_it1.2583.098175
X-RAY DIFFRACTIONr_rigid_bond_restr0.9433608
X-RAY DIFFRACTIONr_sphericity_free22.18513
X-RAY DIFFRACTIONr_sphericity_bonded8.7635631
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 65 -
Rwork0.333 1223 -
all-1288 -
obs--90.45 %

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