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Yorodumi- PDB-1efz: MUTAGENESIS AND CRYSTALLOGRAPHIC STUDIES OF ZYMOMONAS MOBILIS TRN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1efz | ||||||
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Title | MUTAGENESIS AND CRYSTALLOGRAPHIC STUDIES OF ZYMOMONAS MOBILIS TRNA-GUANINE TRANSGLYCOSYLASE TO ELUCIDATE THE ROLE OF SERINE 103 FOR ENZYMATIC ACTIVITY | ||||||
Components | TRNA-GUANINE TRANSGLYCOSYLASE | ||||||
Keywords | TRANSFERASE / TRNA-MODIFYING ENZYME / GLYCOSYLTRANSFERASE | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Gradler, U. / Ficner, R. / Garcia, G.A. / Stubbs, M.T. / Klebe, G. / Reuter, K. | ||||||
Citation | Journal: FEBS Lett. / Year: 1999 Title: Mutagenesis and crystallographic studies of Zymomonas mobilis tRNA-guanine transglycosylase to elucidate the role of serine 103 for enzymatic activity. Authors: Gradler, U. / Ficner, R. / Garcia, G.A. / Stubbs, M.T. / Klebe, G. / Reuter, K. #1: Journal: Embo J. / Year: 1996 Title: Crystal Structure of tRNA-Guanine Transglycosylase: RNA Modification by Base Exchange. Authors: Romier, C. / Reuter, K. / Suck, D. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1efz.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1efz.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 1efz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/1efz ftp://data.pdbj.org/pub/pdb/validation_reports/ef/1efz | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42909.703 Da / Num. of mol.: 1 / Mutation: S103A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis (bacteria) / Plasmid: PET9D / Production host: Escherichia coli (E. coli) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-PRF / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.03 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, tris, dtt, dmso, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 27, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→71 Å / Num. obs: 27018 / Observed criterion σ(F): 2 / Observed criterion σ(I): 0.001 / Rmerge(I) obs: 0.057 |
Reflection | *PLUS % possible obs: 97.4 % |
-Processing
Software |
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Refinement | Resolution: 2→71 Å / σ(F): 2 / σ(I): 0.001
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Refinement step | Cycle: LAST / Resolution: 2→71 Å
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Refine LS restraints |
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