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- PDB-1zkw: Crystal structure of Arg347Ala mutant of botulinum neurotoxin E c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1zkw | ||||||
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Title | Crystal structure of Arg347Ala mutant of botulinum neurotoxin E catalytic domain | ||||||
![]() | botulinum neurotoxin type E | ||||||
![]() | HYDROLASE / botulinum neurotoxin E / Arg347Ala mutant / catalytic domain | ||||||
Function / homology | ![]() Toxicity of botulinum toxin type E (botE) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane ...Toxicity of botulinum toxin type E (botE) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Agarwal, R. / Binz, T. / Swaminathan, S. | ||||||
![]() | ![]() Title: Analysis of Active Site Residues of Botulinum Neurotoxin E by Mutational, Functional, and Structural Studies: Glu335Gln Is an Apoenzyme. Authors: Agarwal, R. / Binz, T. / Swaminathan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.3 KB | Display | ![]() |
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PDB format | ![]() | 140.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435 KB | Display | ![]() |
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Full document | ![]() | 458.6 KB | Display | |
Data in XML | ![]() | 34.5 KB | Display | |
Data in CIF | ![]() | 47.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zkxC ![]() 1zl5C ![]() 1zl6C ![]() 1zn3C ![]() 1t3aS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 47601.664 Da / Num. of mol.: 2 / Fragment: catalytic domain (residues 2-421) / Mutation: R347A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: Ammonium sulfate, Lithium sulfate, Sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Apr 1, 2004 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. all: 72275 / Num. obs: 72275 / % possible obs: 82.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5 / Num. unique all: 4723 / % possible all: 59.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1T3A Resolution: 2.17→42.35 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 146532.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: In general, three loop regions (50-65, 188-200 and 234-244) are either disordered or have very weak electron density in both chains. In this entry, the missing residues are due to the ...Details: In general, three loop regions (50-65, 188-200 and 234-244) are either disordered or have very weak electron density in both chains. In this entry, the missing residues are due to the absence of interpretable electron density in those regions.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.0674 Å2 / ksol: 0.370535 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.17→42.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.31 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
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Xplor file |
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