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- PDB-4lbu: tRNA guanine transglycosylase (TGT) in complex with Furanoside-Ba... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lbu | ||||||
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Title | tRNA guanine transglycosylase (TGT) in complex with Furanoside-Based lin-Benzoguanine 2 | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Tim Barrel / GLYCOSYLTRANSFERASE / Zinc-BINDING / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Replacement of Water Molecules in a Phosphate Binding Site by Furanoside-Appended lin-Benzoguanine Ligands of tRNA-Guanine Transglycosylase (TGT). Authors: Barandun, L.J. / Ehrmann, F.R. / Zimmerli, D. / Immekus, F. / Giroud, M. / Grunenfelder, C. / Schweizer, W.B. / Bernet, B. / Betz, M. / Heine, A. / Klebe, G. / Diederich, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.5 KB | Display | ![]() |
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PDB format | ![]() | 141.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 808.9 KB | Display | ![]() |
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Full document | ![]() | 811.3 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kwoC ![]() 4leqC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43069.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pPR-IBA2 / Production host: ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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-Non-polymers , 5 types, 441 molecules ![](data/chem/img/1WJ.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-1WJ / | ||||
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#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.72 % |
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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, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 17, 2012 / Details: RH-COATED SILICON WITH INDIRECT WATER COOLING |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85507 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→50 Å / Num. all: 136269 / Num. obs: 136269 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 11.9 Å2 / Rsym value: 0.043 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.17→1.19 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 6654 / Rsym value: 0.48 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PUD Resolution: 1.17→14.91 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.17→14.91 Å
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Refine LS restraints |
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LS refinement shell |
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