+Open data
-Basic information
Entry | Database: PDB / ID: 4kyp | ||||||
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Title | Beta-Scorpion Toxin folded in the periplasm of E.coli | ||||||
Components | Beta-insect excitatory toxin Bj-xtrIT | ||||||
Keywords | TOXIN / Alpha-Beta / Venom / Voltage Gated Na-Channels | ||||||
Function / homology | Function and homology information sodium channel inhibitor activity / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Hottentotta judaicus (scorpion) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | O'Reilly, A.O. / Cole, A.R. / Lopes, J.L. / Lampert, A. / Wallace, B.A. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2014 Title: Chaperone-mediated native folding of a beta-scorpion toxin in the periplasm of Escherichia coli. Authors: O'Reilly, A.O. / Cole, A.R. / Lopes, J.L. / Lampert, A. / Wallace, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kyp.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kyp.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 4kyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/4kyp ftp://data.pdbj.org/pub/pdb/validation_reports/ky/4kyp | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9439.647 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hottentotta judaicus (scorpion) / Gene: XTRIT / Production host: Escherichia coli (E. coli) / References: UniProt: P56637 #2: Chemical | #3: Chemical | ChemComp-PG4 / | #4: 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: 2.25 Å3/Da / Density % sol: 45.42 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2M NaCl, Bis-Tris, 29% PEG 3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2012 |
Radiation | Monochromator: channel cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.28 Å / Num. all: 26392 / Num. obs: 26392 / % possible obs: 69.23 % / Observed criterion σ(F): 1.48 / Observed criterion σ(I): 1.22 / Biso Wilson estimate: 20.05 Å2 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 1.22 / % possible all: 9.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.28 Å / Cor.coef. Fo:Fc: 0.9112 / Cor.coef. Fo:Fc free: 0.8947 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24.28 Å2
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Refine analyze | Luzzati coordinate error obs: 0.199 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→44.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.77 Å / Total num. of bins used: 13
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