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Yorodumi- PDB-7jwq: Fab CJ11 in complex IL-1beta peptide liberated by Caspase cleavage -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jwq | ||||||
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Title | Fab CJ11 in complex IL-1beta peptide liberated by Caspase cleavage | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IL-1beta / caspase | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||
Authors | Payandeh, J. / Ho, H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Discovery of a caspase cleavage motif antibody reveals insights into noncanonical inflammasome function. Authors: Davies, C.W. / Stowe, I. / Phung, Q.T. / Ho, H. / Bakalarski, C.E. / Gupta, A. / Zhang, Y. / Lill, J.R. / Payandeh, J. / Kayagaki, N. / Koerber, J.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jwq.cif.gz | 317.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jwq.ent.gz | 262 KB | Display | PDB format |
PDBx/mmJSON format | 7jwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jwq_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
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Full document | 7jwq_full_validation.pdf.gz | 436.9 KB | Display | |
Data in XML | 7jwq_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 7jwq_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/7jwq ftp://data.pdbj.org/pub/pdb/validation_reports/jw/7jwq | HTTPS FTP |
-Related structure data
Related structure data | 7jwpC 5i8oS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23001.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #2: Antibody | Mass: 23397.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #3: Protein/peptide | Mass: 768.853 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Water | ChemComp-HOH / | |
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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: 2.53 Å3/Da / Density % sol: 51.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate pH 6.5, 18% PEG8000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 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→30 Å / Num. obs: 54078 / % possible obs: 85.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.97 |
Reflection shell | Resolution: 2→2.04 Å / Rmerge(I) obs: 0.681 / Num. unique obs: 500 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I8O Resolution: 2.001→29.527 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.63 / 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: 127.52 Å2 / Biso mean: 46.1521 Å2 / Biso min: 21.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.001→29.527 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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