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- PDB-6yht: A lid blocking mechanism of a cone snail toxin revealed at the at... -

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Basic information

Entry
Database: PDB / ID: 6yht
TitleA lid blocking mechanism of a cone snail toxin revealed at the atomic level
ComponentsConk-C1
KeywordsTOXIN / conkunitzin-3
Function / homologyCITRIC ACID
Function and homology information
Biological speciesConus cocceus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSaikia, C. / Altman-Gueta, H. / Dym, O. / Frolow, F. / Gurevitz, M. / Gordon, D. / Reuveny, E. / Karbat, I.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1248/15 Israel
CitationJournal: J.Mol.Biol. / Year: 2021
Title: A Molecular Lid Mechanism of K + Channel Blocker Action Revealed by a Cone Peptide.
Authors: Saikia, C. / Dym, O. / Altman-Gueta, H. / Gordon, D. / Reuveny, E. / Karbat, I.
History
DepositionMar 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conk-C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0504
Polymers6,6651
Non-polymers3843
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-9 kcal/mol
Surface area3980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.609, 68.609, 68.609
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-101-

SO4

21A-101-

SO4

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Components

#1: Protein Conk-C1


Mass: 6665.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus cocceus (invertebrata) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.04 Å3/Da / Density % sol: 69.54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.100M Sodium citrate tribasic dihydrate pH 5.6 20.00% v/v Isopropanol 20.00% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→39.61 Å / Num. obs: 12142 / % possible obs: 99.97 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.02 / Rrim(I) all: 0.027 / Net I/σ(I): 20.58
Reflection shellResolution: 2.15→2.227 Å / Rmerge(I) obs: 0.3515 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 1206 / CC1/2: 0.695 / Rpim(I) all: 0.3515 / Rrim(I) all: 0.4971 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y62

1y62


Resolution: 2.15→39.61 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 562 4.95 %
Rwork0.2056 10800 -
obs0.2064 11362 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.67 Å2 / Biso mean: 63.6919 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.15→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms438 0 20 10 468
Biso mean--82.72 56.97 -
Num. residues----56
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.15-2.370.31741480.272227152863
2.37-2.710.29421420.275626712813
2.71-3.410.29541360.250127012837
3.41-39.610.1751360.173527132849

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