+Open data
-Basic information
Entry | Database: PDB / ID: 6f0o | ||||||
---|---|---|---|---|---|---|---|
Title | Botulinum neurotoxin A3 Hc domain | ||||||
Components | Bontoxilysin A | ||||||
Keywords | TOXIN / botulinum neurotoxin A3 subtype / A3 / binding domain / Hc domain | ||||||
Function / homology | Function and homology information negative regulation of neurotransmitter secretion / bontoxilysin / protein transmembrane transporter activity / : / metalloendopeptidase activity / toxin activity / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Davies, J.R. / Liu, S.M. / Acharya, K.R. | ||||||
Citation | Journal: J. Struct. Biol. / Year: 2018 Title: High resolution crystal structures of Clostridium botulinum neurotoxin A3 and A4 binding domains. Authors: Davies, J.R. / Rees, J. / Liu, S.M. / Acharya, K.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6f0o.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6f0o.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 6f0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f0o_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6f0o_full_validation.pdf.gz | 454.5 KB | Display | |
Data in XML | 6f0o_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 6f0o_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/6f0o ftp://data.pdbj.org/pub/pdb/validation_reports/f0/6f0o | HTTPS FTP |
-Related structure data
Related structure data | 6f0pC 2vuaS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50464.461 Da / Num. of mol.: 1 / Fragment: Hc domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (strain Loch Maree / Type A3) (bacteria) Gene: botA, CLK_A0076 / Production host: Escherichia coli (E. coli) / References: UniProt: B1L2G5, bontoxilysin |
---|---|
#2: Chemical | ChemComp-PPI / |
#3: Chemical | ChemComp-1PE / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.67 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MIB pH 4.0, 25% w/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→96.47 Å / Num. obs: 55445 / % possible obs: 96.9 % / Redundancy: 12.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.036 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.352 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2169 / CC1/2: 0.639 / Rpim(I) all: 0.639 / % possible all: 79.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2vua Resolution: 1.6→72.81 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.892 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.093 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.573 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→72.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|