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- PDB-5jgm: tRNA guanine Transglycosylase (TGT) in co-crystallized complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jgm | ||||||
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Title | tRNA guanine Transglycosylase (TGT) in co-crystallized complex with ethyl (2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-6-yl)carbamate | ||||||
![]() | Queuine tRNA-ribosyltransferase![]() | ||||||
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Function / homology | ![]() tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ehrmann, F.R. / Nguyen, D. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Carbamate-protected lin-Benzoguanines as promising candidates for improving solubility and membrane permeability Authors: Ehrmann, F.R. / Hohn, C. / Heine, A. / Reuter, K. / Diederich, F. / 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 | ![]() | 182.9 KB | Display | ![]() |
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PDB format | ![]() | 143.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5jgoC ![]() 1p0dS S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 42925.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Production host: ![]() ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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-Non-polymers , 6 types, 442 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/810.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/810.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ChemComp-ZN / | #4: Chemical | ![]() #5: Chemical | ChemComp-810 / | #6: Chemical | ChemComp-CL / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.77 % |
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Crystal grow![]() | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 13% PEG 8000,100mM MES, 1mM DTT, 10% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.38→45.29 Å / Num. obs: 84560 / % possible obs: 98.9 % / Redundancy: 3.4 % / Rsym value: 0.041 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.38→1.46 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.2 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1P0D Resolution: 1.38→43.85 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→43.85 Å
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Refine LS restraints |
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LS refinement shell |
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