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

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Basic information

Entry
Database: PDB / ID: 6yhy
TitleA lid blocking mechanism of a cone snail toxin revealed at the atomic level
ComponentsConk-S1
KeywordsTOXIN / Conk-S1
Function / homology
Function and homology information


potassium channel regulator activity / serine-type endopeptidase inhibitor activity / toxin activity / extracellular region
Similarity search - Function
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
Similarity search - Domain/homology
Kunitz-type conkunitzin-S1
Similarity search - Component
Biological speciesConus consors (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / entity / entity_name_com / entity_src_gen / pdbx_database_proc / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
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 / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
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-S1
B: Conk-S1


Theoretical massNumber of molelcules
Total (without water)13,7252
Polymers13,7252
Non-polymers00
Water1,44180
1
A: Conk-S1


Theoretical massNumber of molelcules
Total (without water)6,8621
Polymers6,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Conk-S1


Theoretical massNumber of molelcules
Total (without water)6,8621
Polymers6,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.776, 52.285, 56.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Conk-S1


Mass: 6862.458 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus consors (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C1X2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
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: 1.55→19.13 Å / Num. obs: 35688 / % possible obs: 98.35 % / Redundancy: 4.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.028 / Rrim(I) all: 0.039 / Net I/σ(I): 17.26
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.4133 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 3386 / CC1/2: 0.587 / Rpim(I) all: 0.4133 / Rrim(I) all: 0.5845 / % possible all: 94.81

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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: 1.55→19.13 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.18
RfactorNum. reflection% reflection
Rfree0.2249 1686 5.04 %
Rwork0.1904 --
obs0.1922 33433 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.07 Å2 / Biso mean: 23.3189 Å2 / Biso min: 11.82 Å2
Refinement stepCycle: final / Resolution: 1.55→19.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 0 80 1024
Biso mean---31.83 -
Num. residues----118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.60.3361610.29422555271694
1.6-1.650.3211170.2782668278598
1.65-1.710.28811560.25942654281098
1.71-1.780.27471370.23782631276898
1.78-1.860.24881440.21672688283298
1.86-1.960.20881510.19632635278698
1.96-2.080.21891320.18482692282498
2.08-2.240.24081410.19182657279898
2.24-2.460.30451380.19632661279998
2.46-2.820.24441240.19432707283199
2.82-3.550.20491510.18432649280098
3.55-19.130.17481340.15732550268494

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