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Yorodumi- PDB-6hox: Crystal structure of the binding domain of Paraclostridial Mosqui... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hox | ||||||
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Title | Crystal structure of the binding domain of Paraclostridial Mosquitocidal Protein 1 | ||||||
Components | Binding domain (Hc) of Paraclostridial Mosquitocidal Protein 1 | ||||||
Keywords | TOXIN / neurotoxin / botulinum / Paraclostridium bifermentans / Anopheles | ||||||
Function / homology | Function and homology information negative regulation of neurotransmitter secretion / : / metallopeptidase activity / extracellular region Similarity search - Function | ||||||
Biological species | Paraclostridium bifermentans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Masuyer, G. / Stenmark, P. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: A neurotoxin that specifically targets Anopheles mosquitoes. Authors: Contreras, E. / Masuyer, G. / Qureshi, N. / Chawla, S. / Dhillon, H.S. / Lee, H.L. / Chen, J. / Stenmark, P. / Gill, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hox.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hox.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 6hox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/6hox ftp://data.pdbj.org/pub/pdb/validation_reports/ho/6hox | HTTPS FTP |
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-Related structure data
Related structure data | 4kbbS S: Starting model for refinement |
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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: 52745.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Binding domain (Hc) of Paraclostridial Mosquitocidal Protein 1 Source: (gene. exp.) Paraclostridium bifermentans (bacteria) Strain: Malaysia / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5H1ZR34*PLUS |
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#2: Chemical | ChemComp-PEG / |
#3: Chemical | ChemComp-ACT / |
#4: 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: 2.15 Å3/Da / Density % sol: 42.7 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop Details: 0.12 M Ethylene glycols, 0.1 M Buffer System 3 pH 8.5, 50 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.984 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.46 Å / Num. obs: 31355 / % possible obs: 96.9 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.093 / Rrim(I) all: 0.135 / Χ2: 0.97 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2098 / CC1/2: 0.641 / Rpim(I) all: 0.7 / Rrim(I) all: 1.009 / Χ2: 0.95 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KBB Resolution: 1.95→48.46 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.622 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.15 / 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: 33.866 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→48.46 Å
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Refine LS restraints |
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