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Yorodumi- PDB-5t8y: Structure of epoxyqueuosine reductase from Bacillus subtilis with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t8y | |||||||||
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Title | Structure of epoxyqueuosine reductase from Bacillus subtilis with the Asp134 catalytic loop swung out of the active site. | |||||||||
Components |
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Keywords | OXIDOREDUCTASE/RNA / B12 / cobalamin / iron sulfur cluster / tRNA modifying enzyme / 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: 2.653 Å | |||||||||
Authors | Dowling, D.P. / Miles, Z.D. / Kohrer, C. / Maiocco, S.J. / Elliott, S.J. / 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 | 5t8y.cif.gz | 173.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t8y.ent.gz | 130.6 KB | Display | PDB format |
PDBx/mmJSON format | 5t8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/5t8y ftp://data.pdbj.org/pub/pdb/validation_reports/t8/5t8y | HTTPS FTP |
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-Related structure data
Related structure data | 5d08SC 5d0aC 5d0bC 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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2 |
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Unit cell |
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-Components
-Protein / RNA chain , 2 types, 3 molecules ABX
#1: Protein | Mass: 48736.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: queG, ygaP, yhbA, BSU08910 / Production host: Escherichia coli (E. coli) / References: UniProt: P97030, epoxyqueuosine reductase #2: RNA chain | | Mass: 5427.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: anticodon stem loop of Tyr-tRNA from E. coli / Source: (synth.) Escherichia coli (E. coli) |
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-Non-polymers , 4 types, 27 molecules
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | ChemComp-PO4 / #6: 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: 2.29 Å3/Da / Density % sol: 46.25 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M acetate (pH 4.5), 0.4 M (NH4)H2PO4, 12% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 25487 / % possible obs: 95.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.95 / % possible all: 79 |
-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: 2.653→47.9 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 37.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.46 Å2 / Biso mean: 71.4087 Å2 / Biso min: 58.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.653→47.9 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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