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Yorodumi- PDB-4wfs: Crystal Structure of tRNA-dihydrouridine(20) synthase catalytic domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wfs | ||||||
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Title | Crystal Structure of tRNA-dihydrouridine(20) synthase catalytic domain | ||||||
Components | tRNA-dihydrouridine(20) synthase [NAD(P)+]-like | ||||||
Keywords | OXIDOREDUCTASE / RNA BINDING PROTEIN / tRNA PROCESSING / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / tRNA modification in the nucleus and cytosol / protein kinase inhibitor activity / antiviral innate immune response / NADPH binding / PKR-mediated signaling / double-stranded RNA binding ...tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / tRNA modification in the nucleus and cytosol / protein kinase inhibitor activity / antiviral innate immune response / NADPH binding / PKR-mediated signaling / double-stranded RNA binding / FMN binding / flavin adenine dinucleotide binding / tRNA binding / endoplasmic reticulum / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Bou-Nader, C. / Pecqueur, L. / Kamah, A. / Bregeon, D. / Golinelli-Pimpaneau, B. / Guimaraes, B.G. / Fontecave, M. / Hamdane, D. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: An extended dsRBD is required for post-transcriptional modification in human tRNAs. Authors: Bou-Nader, C. / Pecqueur, L. / Bregeon, D. / Kamah, A. / Guerineau, V. / Golinelli-Pimpaneau, B. / Guimaraes, B.G. / Fontecave, M. / Hamdane, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wfs.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wfs.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 4wfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wfs_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4wfs_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4wfs_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 4wfs_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/4wfs ftp://data.pdbj.org/pub/pdb/validation_reports/wf/4wfs | HTTPS FTP |
-Related structure data
Related structure data | 4wftC 3b0pS 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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Unit cell |
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-Components
#1: Protein | Mass: 36805.359 Da / Num. of mol.: 1 / Fragment: DUS domain, UNP residues 14-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUS2, DUS2L / Plasmid: pET11d / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): STAR codon plus References: UniProt: Q9NX74, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor | ||||
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#2: Chemical | ChemComp-FMN / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 58.85 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: Protein 8 mg/mL in Tris 25 mM pH 8.0 NaCl 150 mM Precipitant: Ammonium sulfate 2.2 M, isopropanol 2% v/v |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2012 |
Radiation | Monochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→43.64 Å / Num. obs: 12686 / % possible obs: 99.09 % / Redundancy: 7.2 % / Biso Wilson estimate: 54.9 Å2 / Net I/σ(I): 19.87 |
Reflection shell | Resolution: 2.68→2.77 Å / Redundancy: 7.12 % / Mean I/σ(I) obs: 2.69 / % possible all: 91.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B0P Resolution: 2.68→43.64 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9227 / SU R Cruickshank DPI: 0.484 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.494 / SU Rfree Blow DPI: 0.258 / SU Rfree Cruickshank DPI: 0.26
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Displacement parameters | Biso mean: 53.9 Å2
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Refine analyze | Luzzati coordinate error obs: 0.337 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.68→43.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.68→2.94 Å / Total num. of bins used: 6
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