+Open data
-Basic information
Entry | Database: PDB / ID: 1wkf | ||||||
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Title | TRNA-GUANINE TRANSGLYCOSYLASE | ||||||
Components | TRNA-GUANINE TRANSGLYCOSYLASE | ||||||
Keywords | TRNA-MODIFYING ENZYME | ||||||
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: 2.2 Å | ||||||
Authors | Romier, C. / Reuter, K. / Suck, D. / Ficner, R. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Mutagenesis and crystallographic studies of Zymomonas mobilis tRNA-guanine transglycosylase reveal aspartate 102 as the active site nucleophile. Authors: Romier, C. / Reuter, K. / Suck, D. / Ficner, R. #1: Journal: Proteins / Year: 1996 Title: Purification, Crystallization, and Preliminary X-Ray Diffraction Studies of tRNA-Guanine Transglycosylase from Zymomonas Mobilis Authors: Romier, C. / Ficner, R. / Reuter, K. / Suck, D. #2: 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. #3: Journal: J.Bacteriol. / Year: 1995 Title: Sequence Analysis and Overexpression of the Zymomonas Mobilis Tgt Gene Encoding tRNA-Guanine Transglycosylase: Purification and Biochemical Characterization of the Enzyme Authors: Reuter, K. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wkf.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wkf.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/1wkf ftp://data.pdbj.org/pub/pdb/validation_reports/wk/1wkf | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 42973.789 Da / Num. of mol.: 1 / Mutation: D156Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: TGT / Plasmid: PET-9D / Gene (production host): TGT / Production host: Escherichia coli (E. coli) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion, hanging dropDetails: Romier, C., (1996) Proteins: Struct.,Funct., Genet., 24, 516. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 14, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 19632 / % possible obs: 93.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.038 |
Reflection | *PLUS Highest resolution: 2.2 Å |
-Processing
Software |
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Refinement | Resolution: 2.2→6 Å / σ(F): 2
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Displacement parameters | Biso mean: 20.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |