+Open data
-Basic information
Entry | Database: PDB / ID: 2mf3 | ||||||
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Title | SGTX-Sf1a | ||||||
Components | U2-segestritoxin-Sf1a | ||||||
Keywords | TOXIN / Spider / ICK / Disulfide / Non-uniform sampling / Maximum entropy / Insecticidal / Heteronuclear | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Segestria florentina (spider) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Mobli, M. / Bende, N.S. / King, G.F. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mf3.cif.gz | 297.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mf3.ent.gz | 252.7 KB | Display | PDB format |
PDBx/mmJSON format | 2mf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mf3_validation.pdf.gz | 417.8 KB | Display | wwPDB validaton report |
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Full document | 2mf3_full_validation.pdf.gz | 491.4 KB | Display | |
Data in XML | 2mf3_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 2mf3_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/2mf3 ftp://data.pdbj.org/pub/pdb/validation_reports/mf/2mf3 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | 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 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Solution structure of the insecticidal spider toxin Sf1a from Segestria florentina. | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Scalar dimensions acquired using NUS and processed using Maximum Entropy reconstruction. NOE dimensions acquired using linear sampling and processed using Linear prediction/DFT. |
-Sample preparation
Details | Contents: 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 | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 20 / pH: 3.5 / Pressure: ambient / Temperature: 313 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 / Details: 15000 steps | ||||||||||||||||||||||||||||
NMR constraints | NOE 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer 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 rms | Distance rms dev: 0 Å / Distance rms dev error: 0 Å |