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Yorodumi- PDB-8weo: Bacteroides fragilis toxin in complex with neutralization nanobody -
+Open data
-Basic information
Entry | Database: PDB / ID: 8weo | ||||||
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Title | Bacteroides fragilis toxin in complex with neutralization nanobody | ||||||
Components |
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Keywords | TOXIN/IMMUNE SYSTEM / Bacteroides fragilis toxin / BFT / Nanobody / TOXIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information fragilysin / metallopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Bacteroides fragilis (bacteria) Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Guo, Y. / Wen, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Bacteroides fragilis toxin in complex with neutralization nanobody Authors: Guo, Y. / Wen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8weo.cif.gz | 264.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8weo.ent.gz | 212.3 KB | Display | PDB format |
PDBx/mmJSON format | 8weo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8weo_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8weo_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8weo_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 8weo_validation.cif.gz | 55 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/8weo ftp://data.pdbj.org/pub/pdb/validation_reports/we/8weo | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20698.967 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: btfP / Production host: Escherichia coli (E. coli) / References: UniProt: P54355, fragilysin #2: Antibody | Mass: 14013.346 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30.42 Å / Num. obs: 222554 / % possible obs: 99.96 % / Redundancy: 12.7 % / CC1/2: 1 / Net I/σ(I): 21.14 |
Reflection shell | Resolution: 1.5→1.554 Å / Num. unique obs: 11227 / CC1/2: 0.512 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30.42 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 22.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→30.42 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.6208 Å / Origin y: -38.5342 Å / Origin z: 16.3877 Å
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Refinement TLS group | Selection details: all |