[English] 日本語
![](img/lk-miru.gif)
- PDB-1zyw: Crystal Structure Of Mutant K8DP9SR58KP60G Of Scorpion alpha-Like... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1zyw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Of Mutant K8DP9SR58KP60G 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 27.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 17.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 445.6 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zu3C ![]() 1zutC ![]() 1zveC ![]() 1zvgC ![]() 1zyvC ![]() 1sn1S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 7344.250 Da / Num. of mol.: 1 / Mutation: K10D, P11S, R60K, P62G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BMK M1 / Plasmid: PVT 102U-ALPHA / Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% (w/v) PEG8000, 0.1M sodium cacodylate pH 6.5, 0.2M ammonium sulfate, 0.02M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
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: 1.3→22.4 Å / Num. all: 13231 / Num. obs: 13231 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 7.8 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.3→1.38 Å / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.152 / % possible all: 99.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1SN1.pdb Resolution: 1.3→22.35 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 961833.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.1665 Å2 / ksol: 0.354135 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→22.35 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.3→1.38 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|