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Yorodumi- PDB-6ezb: Crystal Structure of human tRNA-dihydrouridine(20) synthase catal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ezb | |||||||||
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Title | Crystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain Q305K mutant | |||||||||
Components | tRNA-dihydrouridine(20) synthase [NAD(P)+]-like | |||||||||
Keywords | FLAVOPROTEIN / RNA BINDING PROTEIN / TRNA PROCESSING / OXIDOREDUCTASE | |||||||||
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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Bou-Nader, C. / Bregeon, D. / Pecqueur, L. / Fontecave, M. / Hamdane, D. | |||||||||
Funding support | France, 2items
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Citation | Journal: Biochemistry / Year: 2018 Title: Electrostatic Potential in the tRNA Binding Evolution of Dihydrouridine Synthases. Authors: Bou-Nader, C. / Bregeon, D. / Pecqueur, L. / 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 | 6ezb.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ezb.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ezb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/6ezb ftp://data.pdbj.org/pub/pdb/validation_reports/ez/6ezb | HTTPS FTP |
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-Related structure data
Related structure data | 6ezaC 6ezcC 4xp7S C: citing same article (ref.) S: Starting model for refinement |
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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: 36806.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUS2, DUS2L / Production host: Escherichia coli (E. coli) / Variant (production host): pLysS 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-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.17 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 2.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980105 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980105 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→43.61 Å / Num. obs: 16301 / % possible obs: 93.4 % / Redundancy: 9.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.25→2.45 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.609 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.385 / Rrim(I) all: 1.714 / % possible all: 93.53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XP7 Resolution: 2.25→43.61 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.271 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.27 / SU Rfree Blow DPI: 0.209 / SU Rfree Cruickshank DPI: 0.211
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Displacement parameters | Biso mean: 55.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.25→43.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.4 Å / Total num. of bins used: 39
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Refinement TLS params. | Method: refined / Origin x: -18.7955 Å / Origin y: -24.096 Å / Origin z: -23.0511 Å
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Refinement TLS group | Selection details: { A|* } |