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- PDB-5i5c: X-ray crystal structure of allo-Thr31-ShK -

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Basic information

Entry
Database: PDB / ID: 5i5c
TitleX-ray crystal structure of allo-Thr31-ShK
ComponentsKappa-stichotoxin-She3a
KeywordsTOXIN / allo-Thr31-ShK
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 speciesStichodactyla helianthus (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDang, B. / Kubota, T. / Manda, K.l. / Shen, R. / Bezanilla, F. / Roux, B. / Kent, S.B.H.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Inversion of the Side-Chain Stereochemistry of Indvidual Thr or Ile Residues in a Protein Molecule: Impact on the Folding, Stability, and Structure of the ShK Toxin.
Authors: Dang, B. / Shen, R. / Kubota, T. / Mandal, K. / Bezanilla, F. / Roux, B. / Kent, S.B.
History
DepositionFeb 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Sep 27, 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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kappa-stichotoxin-She3a
B: Kappa-stichotoxin-She3a
C: Kappa-stichotoxin-She3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,70010
Polymers12,2103
Non-polymers4907
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-66 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.743, 46.229, 40.064
Angle α, β, γ (deg.)90.00, 108.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Kappa-stichotoxin-She3a / Kappa-SHTX-She3a / Potassium channel toxin ShK


Mass: 4069.892 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Stichodactyla helianthus (sea anemone) / References: UniProt: P29187
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.3→38.1 Å / Num. obs: 31126 / % possible obs: 97.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LFQ

4lfq


Resolution: 1.3→38.1 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.073 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1691 1312 5.1 %RANDOM
Rwork0.12738 ---
obs0.12951 24495 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.512 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å2-1.24 Å2
2--1.51 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.3→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms834 0 28 173 1035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.019942
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9051.9891267
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.60518.38731
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.78815199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6381512
X-RAY DIFFRACTIONr_chiral_restr0.7170.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021656
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.8671.027447
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0821.546563
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5061.498495
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.74211.8321606
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.5363942
X-RAY DIFFRACTIONr_sphericity_free56.14560
X-RAY DIFFRACTIONr_sphericity_bonded21.31551035
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 112 -
Rwork0.233 1818 -
obs--99.43 %

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