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- PDB-6q6c: Pore-modulating toxins exploit inherent slow inactivation to bloc... -

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Basic information

Entry
Database: PDB / ID: 6q6c
TitlePore-modulating toxins exploit inherent slow inactivation to block K+ channels
ComponentsKunitz-type conkunitzin-S1
KeywordsTOXIN
Function / homology
Function and homology information


potassium channel regulator activity / serine-type endopeptidase inhibitor activity / toxin activity / extracellular space
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
NITRATE ION / PHOSPHATE ION / Kunitz-type conkunitzin-S1
Similarity search - Component
Biological speciesConus striatus (striated cone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKarbat, I. / Gueta, H. / Fine, S. / Szanto, T. / Hamer-Rogotner, S. / Dym, O. / Frolow, F. / Gordon, D. / Panyi, G. / Gurevitz, M. / Reuveny, E.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1248/2015 Israel
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Pore-modulating toxins exploit inherent slow inactivation to block K+channels.
Authors: Karbat, I. / Altman-Gueta, H. / Fine, S. / Szanto, T. / Hamer-Rogotner, S. / Dym, O. / Frolow, F. / Gordon, D. / Panyi, G. / Gurevitz, M. / Reuveny, E.
History
DepositionDec 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kunitz-type conkunitzin-S1
B: Kunitz-type conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,57111
Polymers13,9472
Non-polymers6249
Water2,540141
1
A: Kunitz-type conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3797
Polymers6,9741
Non-polymers4056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kunitz-type conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1934
Polymers6,9741
Non-polymers2193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.835, 64.835, 66.825
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-249-

HOH

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Components

#1: Protein Kunitz-type conkunitzin-S1 / Conk-S1


Mass: 6973.657 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus striatus (striated cone) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C1X2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.05M Potassium phosphate monobasic and 20% w/v PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→28.07 Å / Num. obs: 40174 / % possible obs: 99.41 % / Redundancy: 3.7 % / Rpim(I) all: 0.06148 / Net I/σ(I): 19.75
Reflection shellResolution: 1.3→1.346 Å / Redundancy: 3.7 % / Num. unique obs: 3932 / Rpim(I) all: 0.714 / % possible all: 98.84

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Epinormdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y62

1y62


Resolution: 1.3→28.07 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.336 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20248 2022 5 %RANDOM
Rwork0.16158 ---
obs0.16361 38155 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.632 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.47 Å20 Å2
2--0.93 Å2-0 Å2
3----3.03 Å2
Refinement stepCycle: 1 / Resolution: 1.3→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 38 141 1112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0410.0141033
X-RAY DIFFRACTIONr_bond_other_d0.0010.018851
X-RAY DIFFRACTIONr_angle_refined_deg2.2171.6971392
X-RAY DIFFRACTIONr_angle_other_deg1.6761.611983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1775126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.09120.43569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3215167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4891513
X-RAY DIFFRACTIONr_chiral_restr0.1230.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021212
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02247
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_it3.3072.023495
X-RAY DIFFRACTIONr_mcbond_other2.492.012494
X-RAY DIFFRACTIONr_mcangle_it3.4713.012624
X-RAY DIFFRACTIONr_mcangle_other3.5823.022625
X-RAY DIFFRACTIONr_scbond_it8.1372.652538
X-RAY DIFFRACTIONr_scbond_other5.192.5513
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1413.582739
X-RAY DIFFRACTIONr_long_range_B_refined4.97324.811130
X-RAY DIFFRACTIONr_long_range_B_other4.85223.8881097
X-RAY DIFFRACTIONr_rigid_bond_restr5.18831884
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 145 -
Rwork0.3 2776 -
obs--98.72 %

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