+Open data
-Basic information
Entry | Database: PDB / ID: 7qs3 | ||||||
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Title | Crystal structure of B30.2 PRYSPRY domain of TRIM16 | ||||||
Components | Tripartite motif-containing protein 16 | ||||||
Keywords | LIGASE / E3 / TRIM / TRIM16 / B30.2 domain / SPRY domain / PRYSPRY domain | ||||||
Function / homology | Function and homology information positive regulation of retinoic acid receptor signaling pathway / NACHT domain binding / : / : / interleukin-1 binding / response to organophosphorus / positive regulation of keratinocyte differentiation / response to growth hormone / response to retinoic acid / positive regulation of interleukin-1 beta production ...positive regulation of retinoic acid receptor signaling pathway / NACHT domain binding / : / : / interleukin-1 binding / response to organophosphorus / positive regulation of keratinocyte differentiation / response to growth hormone / response to retinoic acid / positive regulation of interleukin-1 beta production / RING-type E3 ubiquitin transferase / PML body / transferase activity / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Chaikuad, A. / Zhubi, R. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of B30.2 PRYSPRY domain of TRIM16 Authors: Chaikuad, A. / Zhubi, R. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qs3.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qs3.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 7qs3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/7qs3 ftp://data.pdbj.org/pub/pdb/validation_reports/qs/7qs3 | HTTPS FTP |
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-Related structure data
Related structure data | 6flmS S: Starting model for refinement |
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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: 24573.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM16, EBBP / Plasmid: pGTVL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 References: UniProt: O95361, RING-type E3 ubiquitin transferase | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.22 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 6.5, 0.2M sodium bromide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 18, 2020 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.75→45.69 Å / Num. obs: 26339 / % possible obs: 99.9 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.021 / Rrim(I) all: 0.065 / Net I/σ(I): 16.3 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6flm Resolution: 1.75→45.69 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.612 / SU ML: 0.073 / SU R Cruickshank DPI: 0.0935 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.71 Å2 / Biso mean: 38.628 Å2 / Biso min: 23.76 Å2
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Refinement step | Cycle: final / Resolution: 1.75→45.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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