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- PDB-5j9m: 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: 5j9m | ||||||
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Title | tRNA guanine Transglycosylase (TGT) in co-crystallized complex with 2-(methylamino)-1H-benzo[d]imidazole-5-carboxamide | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE / Benzimidazole-derivatives / shigellosis / 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. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Benzimidazole-based Inhibitors as a Novel Scaffold to Inhibit Z.mobilis TGT and Study Protein Flexibility and the Contributions of Active Site Residues to Binding Affinity of lin-Benzopurines. Authors: Ehrmann, F.R. / Hohn, C. / 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 | ![]() | 180.3 KB | Display | ![]() |
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PDB format | ![]() | 142.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.2 KB | Display | ![]() |
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Full document | ![]() | 452.5 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5j9nC ![]() 5j9oC ![]() 5jt5C ![]() 5jt6C ![]() 5jt7C ![]() 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, 403 molecules ![](data/chem/img/6HD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-6HD / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-EDO / | #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: 49.01 % |
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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: MAR CCD 165 mm / Detector: CCD / Date: Dec 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.895 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→45.21 Å / Num. obs: 93288 / % possible obs: 99.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.045 / Net I/av σ(I): 14.3 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.33→1.41 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.3 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1P0D Resolution: 1.33→45.21 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.16 / 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: 1.33→45.21 Å
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Refine LS restraints |
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LS refinement shell |
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