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- PDB-4lfs: High resolution x-ray structure of racemic ShK toxin -

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Basic information

Entry
Database: PDB / ID: 4lfs
TitleHigh resolution x-ray structure of racemic ShK toxin
ComponentsPotassium channel toxin ShK
KeywordsTOXIN / ShK toxin / chemical protein synthesis / racemic protein crystallography
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 / AB INITIO PHASING / Resolution: 0.97 Å
AuthorsDang, B. / Kubota, T. / Mandal, K. / Bezanilla, F. / Kent, S.B.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Native Chemical Ligation at Asx-Cys, Glx-Cys: Chemical Synthesis and High-Resolution X-ray Structure of ShK Toxin by Racemic Protein Crystallography.
Authors: Dang, B. / Kubota, T. / Mandal, K. / Bezanilla, F. / Kent, S.B.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
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 ShK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3046
Polymers4,0701
Non-polymers2345
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.912, 51.653, 21.065
Angle α, β, γ (deg.)90.00, 104.51, 90.00
Int Tables number14
Space group name H-MP121/c1
Detailsbiological unit is the same as asym.

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Components

#1: Protein/peptide Potassium channel toxin ShK


Mass: 4069.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical Synthesis / Source: (synth.) Stichodactyla helianthus (sea anemone) / References: UniProt: P29187
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris, pH 8.5, 25 % Polyethylene glycol 3,350, 20 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.688 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688 Å / Relative weight: 1
ReflectionResolution: 0.97→50 Å / Num. obs: 35825 / % possible obs: 94.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
0.97-0.994.90.339189.6
0.99-15.20.319189.4
1-1.025.20.304193.9
1.02-1.045.20.278192.6
1.04-1.0750.252192.6
1.07-1.094.90.254194
1.09-1.124.80.235190.2
1.12-1.155.10.217196.3
1.15-1.185.10.21194.1
1.18-1.2250.192197
1.22-1.2750.185195.2
1.27-1.324.70.173192.8
1.32-1.385.10.165196.9
1.38-1.455.20.151197.6
1.45-1.545.10.134197.7
1.54-1.664.90.132196.4
1.66-1.835.20.117196.3
1.83-2.095.30.109197.9
2.09-2.634.90.1195.8
2.63-505.10.099196.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXdev_1313refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.97→25.826 Å / Occupancy max: 1 / Occupancy min: 0.07 / SU ML: 0.04 / σ(F): 1.36 / Phase error: 8.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.158 1753 4.97 %
Rwork0.144 --
obs0.1447 35303 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 7.3638 Å2
Refinement stepCycle: LAST / Resolution: 0.97→25.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms278 0 10 75 363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007326
X-RAY DIFFRACTIONf_angle_d1.416430
X-RAY DIFFRACTIONf_dihedral_angle_d11.055134
X-RAY DIFFRACTIONf_chiral_restr0.07645
X-RAY DIFFRACTIONf_plane_restr0.00653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9696-0.99580.1772950.15912405X-RAY DIFFRACTION87
0.9958-1.02510.15641340.14892517X-RAY DIFFRACTION93
1.0251-1.05820.15421430.14172547X-RAY DIFFRACTION92
1.0582-1.0960.16241550.13732539X-RAY DIFFRACTION94
1.096-1.13990.12791350.11972545X-RAY DIFFRACTION93
1.1399-1.19170.12351420.11252608X-RAY DIFFRACTION95
1.1917-1.25460.15281270.11362633X-RAY DIFFRACTION96
1.2546-1.33320.12291260.11162576X-RAY DIFFRACTION94
1.3332-1.43610.13621440.11832644X-RAY DIFFRACTION97
1.4361-1.58060.12771290.1192663X-RAY DIFFRACTION97
1.5806-1.80930.13111340.1332641X-RAY DIFFRACTION96
1.8093-2.27930.17241390.15052643X-RAY DIFFRACTION97
2.2793-25.83570.19861500.19092589X-RAY DIFFRACTION95

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