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Yorodumi- PDB-5d0a: Crystal structure of epoxyqueuosine reductase with cleaved RNA st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d0a | |||||||||
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Title | Crystal structure of epoxyqueuosine reductase with cleaved RNA stem loop | |||||||||
Components |
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Keywords | oxidoreductase/RNA / B12 / tRNA modification / HEAT-domain / queuosine / oxidoreductase-RNA complex | |||||||||
Function / homology | Function and homology information 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 | Bacillus subtilis (bacteria) Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | |||||||||
Authors | Dowling, D.P. / Miles, Z.D. / Kohrer, C. / Bandarian, V. / Drennan, C.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d0a.cif.gz | 358.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d0a.ent.gz | 282.4 KB | Display | PDB format |
PDBx/mmJSON format | 5d0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d0a_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5d0a_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5d0a_validation.xml.gz | 63.5 KB | Display | |
Data in CIF | 5d0a_validation.cif.gz | 90.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/5d0a ftp://data.pdbj.org/pub/pdb/validation_reports/d0/5d0a | HTTPS FTP |
-Related structure data
Related structure data | 5d08SC 5d0bC 5t8yC 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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2 |
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3 |
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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.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: queG, ygaP, yhbA, BSU08910 / Plasmid: pASK-IBA43plus / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P97030, epoxyqueuosine reductase #2: RNA chain | Mass: 5427.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized by IDT / Source: (synth.) Escherichia coli (E. coli) |
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-Non-polymers , 5 types, 814 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
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: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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