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Yorodumi- PDB-5oc4: Crystal structure of human tRNA-dihydrouridine(20) synthase dsRBD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oc4 | ||||||
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Title | Crystal structure of human tRNA-dihydrouridine(20) synthase dsRBD R361A-R362A mutant | ||||||
Components | tRNA-dihydrouridine(20) synthase [NAD(P)+]-like | ||||||
Keywords | RNA BINDING PROTEIN / double-stranded RNA-binding domain | ||||||
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 / NADPH binding / antiviral innate immune response / 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 / NADPH binding / antiviral innate immune response / 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: 1.71 Å | ||||||
Authors | Bou-nader, C. / Pecqueur, L. / Hamdane, D. | ||||||
Funding support | France, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2. Authors: Bou-Nader, C. / Barraud, P. / Pecqueur, L. / Perez, J. / Velours, C. / Shepard, W. / Fontecave, M. / Tisne, C. / Hamdane, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oc4.cif.gz | 38.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oc4.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 5oc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oc4_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 5oc4_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 5oc4_validation.xml.gz | 8 KB | Display | |
Data in CIF | 5oc4_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/5oc4 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/5oc4 | HTTPS FTP |
-Related structure data
Related structure data | 5oc5C 5oc6C 4wftS 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: 13425.269 Da / Num. of mol.: 1 / Mutation: R361A, R362A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUS2, DUS2L / Production host: Escherichia coli BL21(DE3) (bacteria) 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-CL / | ||||
#3: Chemical | #4: Chemical | ChemComp-CAC / | #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: 2.84 Å3/Da / Density % sol: 56.65 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 22% PEG 8K 100 mM sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.52 Å / Num. obs: 16219 / % possible obs: 91.02 % / Redundancy: 5.6 % / Biso Wilson estimate: 31.71 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.2169 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 625 / CC1/2: 0.26 / % possible all: 39.01 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WFT Resolution: 1.71→41.97 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.098 / SU Rfree Blow DPI: 0.093 / SU Rfree Cruickshank DPI: 0.088
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Displacement parameters | Biso mean: 37.02 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.71→41.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.82 Å / Total num. of bins used: 8
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