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- PDB-5i09: tRNA guanine transglycosylase (TGT) in soaked complex with Furano... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i09 | ||||||
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Title | tRNA guanine transglycosylase (TGT) in soaked complex with Furanoside-Based lin-Benzoguanine 3 | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE / soaking / 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: Co-crystallization, Isothermal titration calorimetry and nanoESI-MS reveal dimer disturbing inhibitors Authors: Ehrmann, F.R. / Stojo, J. / Heine, A. / Diederich, F. / Reuter, K. / Sanglier-Cianferani, S. / 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 | ![]() | 180.5 KB | Display | ![]() |
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PDB format | ![]() | 142.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5i00C ![]() 5i02C ![]() 5i03C ![]() 5i06C ![]() 5i07C ![]() 1p0dS 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: 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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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Chemical | ChemComp-1UD / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.21 % |
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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: Jul 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.895 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→45.22 Å / Num. obs: 74015 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rsym value: 0.051 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.44→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.9 / % possible all: 99.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1P0D Resolution: 1.44→23.449 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→23.449 Å
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Refine LS restraints |
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LS refinement shell |
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