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- PDB-6f00: Crystal Structure of human tRNA dihydrouridine synthase (20) dsRB... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f00 | ||||||
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Title | Crystal Structure of human tRNA dihydrouridine synthase (20) dsRBD E423A mutant | ||||||
![]() | tRNA-dihydrouridine(20) synthase [NAD(P)+]-like | ||||||
![]() | RNA BINDING PROTEIN / double-stranded RNA binding domain | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Charles, B.N. / Djemel, H. | ||||||
![]() | ![]() Title: Crystal Structure of human tRNA-dihydrouridine(20) synthase dsRBD E423A mutant Authors: Charles, B.N. / Djemel, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.3 KB | Display | ![]() |
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PDB format | ![]() | 101.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.1 KB | Display | ![]() |
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Full document | ![]() | 464.1 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wftS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13670.661 Da / Num. of mol.: 3 / Mutation: E423A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NX74, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.63 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.6 M ammonium sulfate 100 mM sodium chloride 100 mM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 2.163→44.7 Å / Num. obs: 41560 / % possible obs: 95.99 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.0725 / Net I/σ(I): 7.58 |
Reflection shell | Resolution: 2.163→2.24 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6406 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2174 / CC1/2: 0.481 / % possible all: 92.16 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WFT Resolution: 2.163→44.7 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.19 / Phase error: 25.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.163→44.7 Å
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Refine LS restraints |
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LS refinement shell |
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