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Yorodumi- PDB-5d0b: Crystal structure of epoxyqueuosine reductase with a tRNA-TYR epo... -
+Open data
-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 | |||||||||
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 / tRNA modification / queuosine biosynthetic process / 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: 2.645 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 | 5d0b.cif.gz | 185.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d0b.ent.gz | 138.7 KB | Display | PDB format |
PDBx/mmJSON format | 5d0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d0b_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5d0b_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5d0b_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 5d0b_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/5d0b ftp://data.pdbj.org/pub/pdb/validation_reports/d0/5d0b | HTTPS FTP |
-Related structure data
Related structure data | 5d08SC 5d0aC 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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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.) 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: 5553.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized by IDT and enzymatically modified / Source: (synth.) Escherichia coli (E. coli) |
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-Non-polymers , 5 types, 79 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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