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- PDB-1zyv: Crystal Structure Of Mutant K8DP9SR58KV59G Of Scorpion alpha-Like... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1zyv | ||||||
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Title | Crystal Structure Of Mutant K8DP9SR58KV59G Of Scorpion alpha-Like Neurotoxin Bmk M1 From Buthus Martensii Karsch | ||||||
![]() | Alpha-like neurotoxin BmK-I | ||||||
![]() | TOXIN / SCORPION ALPHA-LIKE TOXIN / BMK M1 / MUTANT / MAMMAL/INSECT SELECTIVITY | ||||||
Function / homology | ![]() sodium channel inhibitor activity / defense response / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ye, X. / Bosmans, F. / Li, C. / Zhang, Y. / Wang, D.C. / Tytgat, J. | ||||||
![]() | ![]() Title: Structural basis for the voltage-gated Na+ channel selectivity of the scorpion alpha-like toxin BmK M1 Authors: Ye, X. / Bosmans, F. / Li, C. / Zhang, Y. / Wang, D.C. / Tytgat, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 26.2 KB | Display | ![]() |
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PDB format | ![]() | 16.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418 KB | Display | ![]() |
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Full document | ![]() | 418 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zu3C ![]() 1zutC ![]() 1zveC ![]() 1zvgC ![]() 1zywC ![]() 1sn1S 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 7342.234 Da / Num. of mol.: 1 / Mutation: K10D, P11S, R60K, V61G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BMK M1 / Plasmid: PVT 102U-ALPHA / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% (w/v) PEG4000, 0.1M Tris-HCl pH 8.5, 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 11, 2004 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→22.5 Å / Num. all: 8962 / Num. obs: 8962 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.5→1.59 Å / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 7.1 / Rsym value: 0.098 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SN1.pdb Resolution: 1.5→22.46 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 627114.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.9434 Å2 / ksol: 0.339323 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→22.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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