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- PDB-1jza: Crystal Structure of Variant 2 Scorpion Toxin from Centruroides s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jza | ||||||
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Title | Crystal Structure of Variant 2 Scorpion Toxin from Centruroides sculpturatus Ewing | ||||||
![]() | NEUROTOXIN 2 | ||||||
![]() | TOXIN / scorpion toxin / noncrystallographic symmetry | ||||||
Function / homology | ![]() sodium channel inhibitor activity / defense response / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cook, W.J. / Zell, A. / Watt, D.D. / Ealick, S.E. | ||||||
![]() | ![]() Title: Structure of variant 2 scorpion toxin from Centruroides sculpturatus Ewing. Authors: Cook, W.J. / Zell, A. / Watt, D.D. / Ealick, S.E. | ||||||
History |
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Remark 999 | SEQUENCE THE AUTHORS MAINTAIN THAT THEIR SEQUENCE IS CORRECT. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.2 KB | Display | ![]() |
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PDB format | ![]() | 24.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.2 KB | Display | ![]() |
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Full document | ![]() | 417.8 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 9.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jzbC ![]() 2sn3S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7182.110 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.02 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.2 Details: 2-methyl-2,4-pentanediol, CHES buffer, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Details: Ealick, S.E., (1984) J. Biol. Chem., 259, 12081. / PH range low: 9.8 / PH range high: 8.6 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ![]() |
Detector | Type: NICOLET / Detector: AREA DETECTOR / Date: Jan 1, 1985 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.8 Å2 |
Reflection shell | Resolution: 2.2→2.34 Å / % possible all: 99.6 |
Reflection | *PLUS Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Rmerge(I) obs: 0.095 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2SN3 Resolution: 2.2→100 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5.6 % / Rfactor obs: 0.255 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.2 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 5.1 % / Rfactor Rwork: 0.319 / Rfactor obs: 0.319 |