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Yorodumi- PDB-6f4e: Crystal structure of the zinc-free catalytic domain of botulinum ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f4e | ||||||
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Title | Crystal structure of the zinc-free catalytic domain of botulinum neurotoxin X | ||||||
Components | Catalytic domain of botulinum neurotoxin X | ||||||
Keywords | TOXIN / botulinum neurotoxin / botulinum toxin / zinc endopeptidase | ||||||
Function / homology | Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / metalloendopeptidase activity / proteolysis / zinc ion binding / DI(HYDROXYETHYL)ETHER / Catalytic domain of botulinum neurotoxin X Function and homology information | ||||||
Biological species | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Masuyer, G. / Henriksson, L. / Kosenina, S. / Zhang, S. / Barkho, S. / Shen, Y. / Dong, M. / Stenmark, P. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Sci Rep / Year: 2018 Title: Structural characterisation of the catalytic domain of botulinum neurotoxin X - high activity and unique substrate specificity. Authors: Masuyer, G. / Zhang, S. / Barkho, S. / Shen, Y. / Henriksson, L. / Kosenina, S. / Dong, M. / Stenmark, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f4e.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f4e.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 6f4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f4e_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
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Full document | 6f4e_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 6f4e_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6f4e_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/6f4e ftp://data.pdbj.org/pub/pdb/validation_reports/f4/6f4e | HTTPS FTP |
-Related structure data
Related structure data | 6f47SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52113.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Recombinant Light Chain (catalytic domain) of botulinum neurotoxin X Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: 111 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A384E149*PLUS |
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#2: Chemical | ChemComp-PEG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 57 % / Description: Plate-like crystal |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 20000, MES pH 6.5, EDTA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.4 Å / Num. obs: 21016 / % possible obs: 93.4 % / Redundancy: 8.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.062 / Rrim(I) all: 0.139 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2059 / CC1/2: 0.691 / Rpim(I) all: 0.52 / Rrim(I) all: 1.11 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F47 Resolution: 2.4→47.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.09 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.27 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.878 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→47.4 Å
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Refine LS restraints |
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