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Yorodumi- PDB-8r5c: Crystal structure of human TRIM7 PRYSPRY domain bound to (2-(1-ox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8r5c | ||||||
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Title | Crystal structure of human TRIM7 PRYSPRY domain bound to (2-(1-oxoisoindolin-2-yl)-3-phenylpropanoyl)-L-glutamine | ||||||
Components | E3 ubiquitin-protein ligase TRIM7 | ||||||
Keywords | LIGASE / TRIM7 / E3-Ligase / Ligand | ||||||
Function / homology | Function and homology information antiviral innate immune response / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / Golgi apparatus / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Munoz Sosa, C.J. / Kraemer, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: Crystal structure of human TRIM7 PRYSPRY domain Authors: Munoz Sosa, C.J. / Kraemer, A. / 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 | 8r5c.cif.gz | 93.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r5c.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 8r5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8r5c_validation.pdf.gz | 810.5 KB | Display | wwPDB validaton report |
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Full document | 8r5c_full_validation.pdf.gz | 813.5 KB | Display | |
Data in XML | 8r5c_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 8r5c_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/8r5c ftp://data.pdbj.org/pub/pdb/validation_reports/r5/8r5c | HTTPS FTP |
-Related structure data
Related structure data | 8r5dC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19746.346 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C029 | ||||||
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#2: Chemical | ChemComp-Y3C / ( | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1 M sodium tartrate, 100 mM citrate pH 5.9 |
-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 EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→39.66 Å / Num. obs: 27677 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.044 / Rrim(I) all: 0.082 / Χ2: 0.69 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.6→1.63 Å / % possible obs: 100 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.444 / Num. measured all: 4524 / Num. unique obs: 1367 / CC1/2: 0.909 / Rpim(I) all: 0.29 / Rrim(I) all: 0.532 / Χ2: 0.25 / Net I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→39.66 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.095 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 mean: 17.368 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→39.66 Å
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