+Open data
-Basic information
Entry | Database: PDB / ID: 5i5c | ||||||
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Title | X-ray crystal structure of allo-Thr31-ShK | ||||||
Components | Kappa-stichotoxin-She3a | ||||||
Keywords | TOXIN / allo-Thr31-ShK | ||||||
Function / homology | ShKT domain / ShKT domain profile. / nematocyst / potassium channel regulator activity / toxin activity / defense response to bacterium / extracellular region / : / Kappa-stichotoxin-She3a Function and homology information | ||||||
Biological species | Stichodactyla helianthus (sea anemone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Dang, B. / Kubota, T. / Manda, K.l. / Shen, R. / Bezanilla, F. / Roux, B. / Kent, S.B.H. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: Inversion of the Side-Chain Stereochemistry of Indvidual Thr or Ile Residues in a Protein Molecule: Impact on the Folding, Stability, and Structure of the ShK Toxin. Authors: Dang, B. / Shen, R. / Kubota, T. / Mandal, K. / Bezanilla, F. / Roux, B. / Kent, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i5c.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i5c.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 5i5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/5i5c ftp://data.pdbj.org/pub/pdb/validation_reports/i5/5i5c | HTTPS FTP |
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-Related structure data
Related structure data | 5i5aC 5i5bC 4lfqS C: citing same article (ref.) 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/peptide | Mass: 4069.892 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Stichodactyla helianthus (sea anemone) / References: UniProt: P29187 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / | #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: 2.22 Å3/Da / Density % sol: 44.53 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS 25% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.7749 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→38.1 Å / Num. obs: 31126 / % possible obs: 97.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.7 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LFQ Resolution: 1.3→38.1 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.073 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 17.512 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→38.1 Å
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Refine LS restraints |
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