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Yorodumi- PDB-6bi5: NMR solution structure of Defensin1 from Centruroides limpidus li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bi5 | ||||||
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Title | NMR solution structure of Defensin1 from Centruroides limpidus limpidus | ||||||
Components | Defensin-1 | ||||||
Keywords | TOXIN / Scorpion / Centruroides limpidus limpidus / Defensin | ||||||
Function / homology | Invertebrate defensins family profile. / Defensin, invertebrate/fungal / defense response to bacterium / innate immune response / extracellular region / Defensin-1 Function and homology information | ||||||
Biological species | Centruroides limpidus (Mexican scorpion) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Escobedo-Gonzalez, F.C. / del Rio-Portilla, F. / Rodriguez-Solano, L.A. | ||||||
Funding support | Mexico, 1items
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Citation | Journal: To Be Published Title: From good defence into mortal risk: NMR studyand conversion of a defensin into a neurotoxin Authors: Escobedo-Gonzalez, F.C. / del Rio-Portilla, F. / Franco-Bodek, D. / Rodriguez-de la Vega, R. / Carrillo-Flores, E. / Rodriguez-Solano, L.A. / Flores-Solis, D. / Garaza-Garcia, A. / Titaux- ...Authors: Escobedo-Gonzalez, F.C. / del Rio-Portilla, F. / Franco-Bodek, D. / Rodriguez-de la Vega, R. / Carrillo-Flores, E. / Rodriguez-Solano, L.A. / Flores-Solis, D. / Garaza-Garcia, A. / Titaux-Delgado, G.A. / Lopez-Vera, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bi5.cif.gz | 182.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bi5.ent.gz | 155 KB | Display | PDB format |
PDBx/mmJSON format | 6bi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bi5_validation.pdf.gz | 378.5 KB | Display | wwPDB validaton report |
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Full document | 6bi5_full_validation.pdf.gz | 475.9 KB | Display | |
Data in XML | 6bi5_validation.xml.gz | 11 KB | Display | |
Data in CIF | 6bi5_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/6bi5 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/6bi5 | HTTPS FTP |
-Related structure data
Related structure data | 6b9wC 6bamC 6bb6C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3609.173 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Centruroides limpidus (Mexican scorpion) Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q6GU94 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 1.3 mM M3D1, 95% H2O/5% D2O / Label: Natural Abundance / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 1.3 mM / Component: M3D1 / Isotopic labeling: natural abundance |
Sample conditions | Ionic strength: .1 Not defined / Label: 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz / Details: 3 mm |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 6 | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 500 / Conformers submitted total number: 20 |