+Open data
-Basic information
Entry | Database: PDB / ID: 5h8d | ||||||
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Title | Crystal structure of an ASC binding nanobody | ||||||
Components | VHH nanobody | ||||||
Keywords | IMMUNE SYSTEM / VHH nanobody / ASC-binding / antibody fragment / inflammasome | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å | ||||||
Authors | Lu, A. / Schmidt, F.I. / Ruan, J. / Tang, C. / Wu, H. / Ploegh, H.L. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2016 Title: A single domain antibody fragment that recognizes the adaptor ASC defines the role of ASC domains in inflammasome assembly. Authors: Schmidt, F.I. / Lu, A. / Chen, J.W. / Ruan, J. / Tang, C. / Wu, H. / Ploegh, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h8d.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h8d.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 5h8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/5h8d ftp://data.pdbj.org/pub/pdb/validation_reports/h8/5h8d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 12253.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
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#2: 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: 3.09 Å3/Da / Density % sol: 60.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1 M citric acid at pH 3.5 and 35% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→68.89 Å / Num. obs: 12777 / % possible obs: 99.2 % / Redundancy: 9.7 % / Net I/σ(I): 8.77 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→68.89 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 18.9 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.79 Å2 / Biso mean: 28.1668 Å2 / Biso min: 11.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.89→68.89 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: -29.2134 Å / Origin y: 10.7299 Å / Origin z: 4.443 Å
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Refinement TLS group |
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