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- PDB-5jsw: 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: 5jsw | ||||||
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Title | tRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-((((3a'R,6'R,6a'R)-2,2,2',2'-tetramethyldihydro-3a'H-spiro[[1,3]dioxolane-4,4'-furo[3,4-d][1,3]dioxol]-6'-yl)methyl)amino)-1H-imidazo[4,5-g]quinazolin-8(7H)-one | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE / co-crystallization / carbohydrates / TRANSFERASE INHIBITOR | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Ehrmann, F.R. / Nguyen, D. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Application of carbohydrates based lin-benzoguanines in a solvent-exposed subpocket of the tRNA-modifying Enzyme TGT Authors: Ehrmann, F.R. / Schaefer, E. / Heine, A. / 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 | ![]() | 186.9 KB | Display | ![]() |
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PDB format | ![]() | 147.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.8 KB | Display | ![]() |
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Full document | ![]() | 464.4 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 30.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jsvC ![]() 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.) ![]() Gene: tgt, ZMO0363 / Production host: ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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-Non-polymers , 6 types, 409 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/6MM.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/6MM.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-6MM / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % |
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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 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→44.89 Å / Num. obs: 114740 / % possible obs: 95.2 % / Redundancy: 4.2 % / Rsym value: 0.041 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.22→1.29 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3 / % possible all: 91.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1P0D Resolution: 1.22→30.163 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→30.163 Å
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Refine LS restraints |
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LS refinement shell |
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