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Yorodumi- PDB-1q2s: Chemical trapping and crystal structure of a catalytic tRNA guani... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q2s | |||||||||
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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 intermediat / Transferase-RNA COMPLEX | |||||||||
Function / homology | Function and homology information tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Zymomonas mobilis (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 | 1q2s.cif.gz | 318.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q2s.ent.gz | 255.7 KB | Display | PDB format |
PDBx/mmJSON format | 1q2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/1q2s ftp://data.pdbj.org/pub/pdb/validation_reports/q2/1q2s | HTTPS FTP |
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-Related structure data
Related structure data | 1q2rC 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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1 |
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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
-RNA chain , 2 types, 2 molecules EF
#1: RNA chain | Mass: 6449.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 6272.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 1 types, 4 molecules ABCD
#3: 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 |
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-Non-polymers , 3 types, 98 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-9DG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.38 % | |||||||||||||||||||||||||||||||||||
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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: 3.2→30 Å / Num. obs: 31891 / Rmerge(I) obs: 0.092 |
Reflection | *PLUS Num. obs: 31940 / % possible obs: 99.7 % / Redundancy: 6.2 % |
Reflection shell | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 3.3 Å / % possible obs: 99.3 % / Redundancy: 4.8 % / Num. unique obs: 3148 / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 4.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1PUD Resolution: 3.2→30 Å / σ(F): 2 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 3.2→30 Å
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Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 26126 / Rfactor Rwork: 0.18 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 3.3 Å / Num. reflection obs: 2270 |