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- PDB-5d0b: Crystal structure of epoxyqueuosine reductase with a tRNA-TYR epo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d0b | |||||||||
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Title | Crystal structure of epoxyqueuosine reductase with a tRNA-TYR epoxyqueuosine-modified tRNA stem loop | |||||||||
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![]() | oxidoreductase/RNA / B12 / tRNA modification / HEAT-domain / queuosine / oxidoreductase-RNA complex | |||||||||
Function / homology | ![]() epoxyqueuosine reductase / epoxyqueuosine reductase activity / queuosine biosynthetic process / tRNA processing / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Dowling, D.P. / Miles, Z.D. / Kohrer, C. / Bandarian, V. / Drennan, C.L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of cobalamin-dependent RNA modification. Authors: Dowling, D.P. / Miles, Z.D. / Kohrer, C. / Maiocco, S.J. / Elliott, S.J. / Bandarian, V. / Drennan, C.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.5 KB | Display | ![]() |
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PDB format | ![]() | 138.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 29.6 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d08SC ![]() 5d0aC ![]() 5t8yC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / RNA chain , 2 types, 3 molecules ABF
#1: Protein | Mass: 48736.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: queG, ygaP, yhbA, BSU08910 / Plasmid: pASK-IBA43plus / Production host: ![]() ![]() #2: RNA chain | | Mass: 5553.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized by IDT and enzymatically modified / Source: (synth.) ![]() ![]() |
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-Non-polymers , 5 types, 79 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.51 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: (0.1 M acetate (pH 4.5), 0.4 M (NH4)H2PO4, 12% (w/v) PEG 3350 Temp details: anaerobic |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.645→100 Å / Num. obs: 26382 / % possible obs: 92.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 37.76 Å2 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.067 / Rrim(I) all: 0.169 / Χ2: 1.108 / Net I/av σ(I): 10 / Net I/σ(I): 5.3 / Num. measured all: 138854 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5D08 Resolution: 2.645→32.049 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.55 Å2 / Biso mean: 31.4805 Å2 / Biso min: 16.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.645→32.049 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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