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- PDB-4lfq: High resolution x-ray crystal structure of L-ShK toxin -

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Basic information

Entry
Database: PDB / ID: 4lfq
TitleHigh resolution x-ray crystal structure of L-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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.059 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 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel toxin ShK


Theoretical massNumber of molelcules
Total (without water)4,0701
Polymers4,0701
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.161, 49.491, 27.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-102-

HOH

21A-105-

HOH

31A-123-

HOH

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.74 Å3/Da / Density % sol: 29.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.1 M DL-Malic acid, pH 7, 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: 1.059→50 Å / Num. obs: 13043 / % possible obs: 98.3 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.06-1.086.30.434198.8
1.08-1.16.60.454197.7
1.1-1.126.50.438196.7
1.12-1.147.40.396199.8
1.14-1.177.60.36199.2
1.17-1.197.60.32199.7
1.19-1.227.60.295199.7
1.22-1.267.50.269199.2
1.26-1.297.20.267198.6
1.29-1.346.90.225196.9
1.34-1.387.80.197199.4
1.38-1.447.80.184199.7
1.44-1.57.70.153199.4
1.5-1.587.50.13198.8
1.58-1.6870.106197.5
1.68-1.817.90.099198.8
1.81-1.997.90.088198.8
1.99-2.287.50.068197.6
2.28-2.887.30.058196.4
2.88-507.40.046193.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_1313refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.059→24.745 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.1 / σ(F): 1.39 / Phase error: 17.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.16 644 4.95 %
Rwork0.1308 --
obs0.1322 13002 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.5693 Å2
Refinement stepCycle: LAST / Resolution: 1.059→24.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms278 0 0 60 338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008314
X-RAY DIFFRACTIONf_angle_d1.275416
X-RAY DIFFRACTIONf_dihedral_angle_d12.871127
X-RAY DIFFRACTIONf_chiral_restr0.06344
X-RAY DIFFRACTIONf_plane_restr0.00553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.059-1.14070.21491300.15382380X-RAY DIFFRACTION96
1.1407-1.25550.17661280.12792484X-RAY DIFFRACTION99
1.2555-1.43720.12581370.11512439X-RAY DIFFRACTION99
1.4372-1.81060.12241180.12692505X-RAY DIFFRACTION99
1.8106-24.75220.1721310.13342550X-RAY DIFFRACTION97

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