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- PDB-2mf3: SGTX-Sf1a -

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Basic information

Entry
Database: PDB / ID: 2mf3
TitleSGTX-Sf1a
ComponentsU2-segestritoxin-Sf1a
KeywordsTOXIN / Spider / ICK / Disulfide / Non-uniform sampling / Maximum entropy / Insecticidal / Heteronuclear
Function / homology
Function and homology information


sodium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Omega-AgatoxinV - #60 / SFI toxin / : / SFI toxin family / Omega-AgatoxinV / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Mu-segestritoxin-Sf1a
Similarity search - Component
Biological speciesSegestria florentina (spider)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsMobli, M. / Bende, N.S. / King, G.F.
CitationJournal: Febs J. / Year: 2015
Title: The insecticidal spider toxin SFI1 is a knottin peptide that blocks the pore of insect voltage-gated sodium channels via a large beta-hairpin loop.
Authors: Bende, N.S. / Dziemborowicz, S. / Herzig, V. / Ramanujam, V. / Brown, G.W. / Bosmans, F. / Nicholson, G.M. / King, G.F. / Mobli, M.
History
DepositionOct 4, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U2-segestritoxin-Sf1a


Theoretical massNumber of molelcules
Total (without water)5,0741
Polymers5,0741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide U2-segestritoxin-Sf1a / U2-SGTX-Sf1a / F5.6 / Toxin SFI 1


Mass: 5073.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Segestria florentina (spider) / Description: HIS-MBP-TEV CLEAVAGE-S-TOXIN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61095
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the insecticidal spider toxin Sf1a from Segestria florentina.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HN(CA)CB
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic
1814D HC(CO)NH
1912D (HB)CB(CGCC)H(ar)
11013D HNCO
NMR detailsText: Scalar dimensions acquired using NUS and processed using Maximum Entropy reconstruction. NOE dimensions acquired using linear sampling and processed using Linear prediction/DFT.

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Sample preparation

DetailsContents: 0.42 mM [U-99% 13C; U-99% 15N] SF1A, 5 % [U-100% 2H] D2O, 20 mM Sodium citrate, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.42 mMSF1A-1[U-99% 13C; U-99% 15N]1
5 %D2O-2[U-100% 2H]1
20 mMSodium citrate-31
Sample conditionsIonic strength: 20 / pH: 3.5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Rownald_NMR_Toolkitv3Jeffrey C. Hochprocessing
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin3Bruker Biospincollection
TALOS+Cornilescu, Delaglio and Baxstructure solution
XEASYBartels et al.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: 15000 steps
NMR constraintsNOE constraints total: 564 / NOE intraresidue total count: 147 / NOE long range total count: 134 / NOE medium range total count: 58 / NOE sequential total count: 225
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å
NMR ensemble rmsDistance rms dev: 0 Å / Distance rms dev error: 0 Å

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