[English] 日本語
Yorodumi- PDB-1zve: Crystal Structure Of Mutant K8G Of Scorpion alpha-Like Neurotoxin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zve | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Of Mutant K8G Of Scorpion alpha-Like Neurotoxin Bmk M1 From Buthus Martensii Karsch | ||||||
Components | Alpha-like neurotoxin BmK-I | ||||||
Keywords | TOXIN / SCORPION ALPHA-LIKE TOXIN / BMK M1 / MUTANT / MAMMAL/INSECT SELECTIVITY | ||||||
Function / homology | Function and homology information sodium channel inhibitor activity / defense response / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Mesobuthus martensii (Chinese scorpion) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Ye, X. / Bosmans, F. / Li, C. / Zhang, Y. / Wang, D.C. / Tytgat, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1zve.cif.gz | 28.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1zve.ent.gz | 17.6 KB | Display | PDB format |
PDBx/mmJSON format | 1zve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/1zve ftp://data.pdbj.org/pub/pdb/validation_reports/zv/1zve | HTTPS FTP |
---|
-Related structure data
Related structure data | 1zu3C 1zutC 1zvgC 1zyvC 1zywC 1sn1S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 7364.328 Da / Num. of mol.: 1 / Mutation: K10G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesobuthus martensii (Chinese scorpion) Gene: BMK M1 / Plasmid: PVT 102U-ALPHA / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): S-78 / References: UniProt: P45697 |
---|---|
#2: Chemical | ChemComp-ACT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% (w/v) PEG4000, 0.1 M Tris-HCl at pH 8.5, 0.2 M sodium acetate , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 25, 2004 |
Radiation | Monochromator: CON-FOCUSE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→31.54 Å / Num. all: 5890 / Num. obs: 5890 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.7→1.81 Å / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.146 / % possible all: 97.6 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SN1.pdb Resolution: 1.7→31.5 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 632455.94 / 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: 42.3865 Å2 / ksol: 0.401609 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.2 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→31.5 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|