+Open data
-Basic information
Entry | Database: PDB / ID: 2atb | ||||||
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Title | Triple mutant 8D9D10V of scorpion toxin LQH-alpha-IT | ||||||
Components | neurotoxin alpha-IT | ||||||
Keywords | TOXIN / alpha toxin / muation / scorpion | ||||||
Function / homology | Function and homology information sodium channel inhibitor activity / defense response / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Leiurus quinquestriatus (Egyptian scorpion) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kahn, R. / Karbat, I. / Gurevitz, M. / Frolow, F. | ||||||
Citation | Journal: To be Published Title: X-ray structures of Lqh-alpha-IT and Lqh-alpha-IT8D9D10V mutant Authors: Kahn, R. / Karbat, I. / Gurevitz, M. / Frolow, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2atb.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2atb.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 2atb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/2atb ftp://data.pdbj.org/pub/pdb/validation_reports/at/2atb | HTTPS FTP |
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-Related structure data
Related structure data | 2ascSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Biologically active in monomeric form |
-Components
#1: Protein | Mass: 7319.305 Da / Num. of mol.: 2 / Mutation: K9D, N10D, Y11V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leiurus quinquestriatus (Egyptian scorpion) Tissue: venom gland / Plasmid: pET-11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P17728 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.01M Cobaltous Chlorid hexahydrate, 0.1M Sodium Acetate trihydrate, 1M of 1,6 Hexnediol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2003 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→65.51 Å / Num. all: 29230 / Num. obs: 29230 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.093 / Χ2: 0.961 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1403 / Rsym value: 0.052 / Χ2: 0.712 / % possible all: 99.5 |
-Phasing
Phasing MR | Rfactor: 0.514 / Cor.coef. Fo:Fc: 0.412
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ASC Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.489 / SU ML: 0.039 / SU R Cruickshank DPI: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.059 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.481 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.599→1.641 Å / Total num. of bins used: 20
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