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- PDB-5d0a: Crystal structure of epoxyqueuosine reductase with cleaved RNA st... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d0a | |||||||||
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Title | Crystal structure of epoxyqueuosine reductase with cleaved RNA 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 | ![]() | 358.2 KB | Display | ![]() |
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PDB format | ![]() | 282.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 63.5 KB | Display | |
Data in CIF | ![]() | 90.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d08SC ![]() 5d0bC ![]() 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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2 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein / RNA chain , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 48736.641 Da / Num. of mol.: 4 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: 5427.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized by IDT / Source: (synth.) ![]() ![]() |
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-Non-polymers , 5 types, 814 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SF4 / #4: Chemical | ChemComp-B12 / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PO4 / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.79 % / Description: square pyramidal |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: (0.1 M acetate, 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: Apr 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 104237 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.15 Å2 / Rsym value: 0.081 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.394 / % possible all: 89.3 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5D08 Resolution: 2.1→46.39 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.85 / 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 mean: 38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.39 Å
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Refine LS restraints |
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LS refinement shell |
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