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Open data
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Basic information
Entry | Database: PDB / ID: 6ygk | ||||||
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Title | TGT Y330F mutant crystallised at pH 8.5 | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE / TGT / TRNA-GUANINE TRANSGLYCOSYLASE / GUANINE INSERTION 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 | ![]() ![]() ![]() | ||||||
![]() | Nguyen, A. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Mutation study on tRNA-guanine transglycosylase for catalysis Testing Authors: Nguyen, A. / Heine, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 275.4 KB | Display | ![]() |
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PDB format | ![]() | 184.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.1 KB | Display | ![]() |
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Full document | ![]() | 428.2 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yfwC ![]() 6yfxC ![]() 1pudS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43053.828 Da / Num. of mol.: 1 / Mutation: T312K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: tgt, ZMO0363 / Production host: ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.68 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM TRIS pH 8.5, 1 mM DTT, 10% (v/v) DMSO, 13% (m/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2019 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→43.4 Å / Num. obs: 77939 / % possible obs: 97.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.02 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.03 |
Reflection shell | Resolution: 1.4→1.48 Å / Num. unique obs: 11334 / CC1/2: 0.853 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PUD Resolution: 1.4→43.4 Å / SU ML: 0.1195 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.5372
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→43.4 Å
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Refine LS restraints |
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LS refinement shell |
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