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Yorodumi- PDB-4hhf: Crystal Structure of chemically synthesized scorpion alpha-toxin OD1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hhf | ||||||
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Title | Crystal Structure of chemically synthesized scorpion alpha-toxin OD1 | ||||||
Components | Alpha-toxin OD1 | ||||||
Keywords | TOXIN / scorpion long-chain alpha-toxin / gating modulator / voltage-gated sodium channels 1.4 / 1.6 / 1.7 / inhibition of fast channel inactivation / C-terminally amidated / venom gland | ||||||
Function / homology | Function and homology information sodium channel inhibitor activity / : / defense response / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Odontobuthus doriae (scorpion) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wang, C.I.A. / Lewis, R.J. / Alewood, P.F. / Durek, T. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Chemical engineering and structural and pharmacological characterization of the alpha-scorpion toxin OD1. Authors: Durek, T. / Vetter, I. / Wang, C.I. / Motin, L. / Knapp, O. / Adams, D.J. / Lewis, R.J. / Alewood, P.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hhf.cif.gz | 38.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hhf.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 4hhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/4hhf ftp://data.pdbj.org/pub/pdb/validation_reports/hh/4hhf | HTTPS FTP |
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-Related structure data
Related structure data | 1sn1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7221.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Odontobuthus doriae (scorpion) / References: UniProt: P84646 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1 uL 20 mg/mL lyophilized toxin in 2 mM hydrochloric acid + 1 uL reservoir (0.1 M Tris-HCl, pH 7.5, 2% v/v dioxane, 56-60% v/v MPD) against 500 uL reservoir (rod-shaped crystals appeared ...Details: 1 uL 20 mg/mL lyophilized toxin in 2 mM hydrochloric acid + 1 uL reservoir (0.1 M Tris-HCl, pH 7.5, 2% v/v dioxane, 56-60% v/v MPD) against 500 uL reservoir (rod-shaped crystals appeared after 24 hours, grew to 0.5 x 0.1 x 0.1 mm), VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→35.1 Å / Num. all: 8454 / Num. obs: 8431 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.21 % / Biso Wilson estimate: 11.76 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 1.54 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 1.5 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SN1 Resolution: 1.8→35.1 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.775 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.11 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.213 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→35.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 4.6911 Å / Origin y: 28.7693 Å / Origin z: 8.0233 Å
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