+Open data
-Basic information
Entry | Database: PDB / ID: 7fd3 | ||||||
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Title | IL-1RAPL2 TIR domain | ||||||
Components | X-linked interleukin-1 receptor accessory protein-like 2 | ||||||
Keywords | IMMUNE SYSTEM / IL-1 family receptor protein / TIR domain | ||||||
Function / homology | Function and homology information interleukin-1, type II, blocking receptor activity / interleukin-1 receptor activity / Receptor-type tyrosine-protein phosphatases / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / regulation of presynapse assembly / central nervous system development / membrane => GO:0016020 / glutamatergic synapse / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Wang, X. / Zhou, J. | ||||||
Citation | Journal: Iscience / Year: 2022 Title: Structural basis of the IL-1 receptor TIR domain-mediated IL-1 signaling Authors: Zhou, J. / Xiao, Y. / Ren, Y. / Ge, J. / Wang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fd3.cif.gz | 45.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fd3.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 7fd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fd3_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 7fd3_full_validation.pdf.gz | 434.7 KB | Display | |
Data in XML | 7fd3_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 7fd3_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/7fd3 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/7fd3 | HTTPS FTP |
-Related structure data
Related structure data | 7fccC 7fchC 7fcjC 7fclC 1t3gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19049.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RAPL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9NP60, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase |
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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: 3.17 Å3/Da / Density % sol: 61.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 8% v/v tacsimate pH5.0, 12% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→49.29 Å / Num. obs: 5452 / % possible obs: 99.8 % / Redundancy: 24 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.99→3.15 Å / Rmerge(I) obs: 1.716 / Num. unique obs: 515 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T3G Resolution: 2.99→49.29 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.84 / 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: 127.97 Å2 / Biso mean: 87.415 Å2 / Biso min: 57.17 Å2 | ||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.99→49.29 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 99 %
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