[English] 日本語
![](img/lk-miru.gif)
- PDB-8agk: Botulinum neurotoxin subtype A6 cell binding domain in complex wi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8agk | ||||||
---|---|---|---|---|---|---|---|
Title | Botulinum neurotoxin subtype A6 cell binding domain in complex with GD1a ganglioside | ||||||
![]() | Bont/A1 | ||||||
![]() | TOXIN / Botulism / ganglioside / botulinum neurotoxin / cell binding domain / complex / subtype | ||||||
Function / homology | ![]() protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gregory, K.S. / Acharya, K.R. / Liu, S.M. / Newell, A.R. / Mojanaga, O.O. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Crystal Structures of the Clostridium botulinum Neurotoxin A6 Cell Binding Domain Alone and in Complex with GD1a Reveal Significant Conformational Flexibility. Authors: Gregory, K.S. / Newell, A.R. / Mojanaga, O.O. / Liu, S.M. / Acharya, K.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 114.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 804.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 807.8 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8alpC ![]() 6twoS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 50681.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-alpha-D-glucopyranose Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source | ||||||
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.74 % |
---|---|
Crystal grow | Temperature: 289.15 K / Method: vapor diffusion / Details: 0.2 M NaCl, 0.1 M HEPES pH 7.0, 20% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→57.65 Å / Num. obs: 67218 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rpim(I) all: 0.05 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 3357 / CC1/2: 0.991 / Rpim(I) all: 2.241 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6TWO Resolution: 1.5→57.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.207 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.087 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.134 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→57.65 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|