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Open data
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Basic information
Entry | Database: PDB / ID: 1wkd | ||||||
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Title | TRNA-GUANINE TRANSGLYCOSYLASE | ||||||
![]() | TRNA-GUANINE TRANSGLYCOSYLASE | ||||||
![]() | TRNA-MODIFYING ENZYME | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() | ||||||
![]() | Romier, C. / Reuter, K. / Suck, D. / Ficner, R. | ||||||
![]() | ![]() 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: ![]() 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: ![]() Title: Crystal Structure of tRNA-Guanine Transglycosylase: RNA Modification by Base Exchange Authors: Romier, C. / Reuter, K. / Suck, D. / Ficner, R. #3: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.7 KB | Display | ![]() |
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PDB format | ![]() | 66 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 367.3 KB | Display | ![]() |
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Full document | ![]() | 374.7 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42881.695 Da / Num. of mol.: 1 / Mutation: D102A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 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 10, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 12629 / % possible obs: 98.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.065 |
Reflection | *PLUS Highest resolution: 2.6 Å |
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Processing
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Refinement | Resolution: 2.6→6 Å / σ(F): 2
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Displacement parameters | Biso mean: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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