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Yorodumi- PDB-1q2r: Chemical trapping and crystal structure of a catalytic tRNA guani... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q2r | |||||||||
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Title | Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate | |||||||||
Components |
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Keywords | Transferase/RNA / TIM barrel / Protein-RNA complex / Covalent intermediate / Transferase-RNA COMPLEX | |||||||||
Function / homology | Function and homology information tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Zymomonas mobilis (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Xie, W. / Liu, X. / Huang, R.H. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate Authors: Xie, W. / Liu, X. / Huang, R.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q2r.cif.gz | 318.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q2r.ent.gz | 255.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/1q2r ftp://data.pdbj.org/pub/pdb/validation_reports/q2/1q2r | HTTPS FTP |
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-Related structure data
Related structure data | 1q2sC 1pudS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: RNA chain | Mass: 6272.784 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Protein | Mass: 42925.703 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis (bacteria) / Strain: ZM4-CP4 / Gene: TGT / Production host: Escherichia coli (E. coli) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-9DG / #5: 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: 2.66 Å3/Da / Density % sol: 53.76 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.069 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 43547 / % possible obs: 99.6 % / Redundancy: 6.6 % |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 98.7 % / Redundancy: 5.1 % / Num. unique obs: 4278 / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 5.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1PUD Resolution: 2.9→30 Å / σ(F): 2 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 36863 / Rfactor Rfree: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / Num. reflection obs: 3280 |