[English] 日本語
![](img/lk-miru.gif)
- PDB-2bbf: Crystal structure of tRNA-guanine transglycosylase (TGT) from Zym... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2bbf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of tRNA-guanine transglycosylase (TGT) from Zymomonas mobilis in complex with 6-amino-3,7-dihydro-imidazo[4,5-g]quinazolin-8-one | ||||||
![]() | tRNA guanine transglycosylase | ||||||
![]() | TRANSFERASE / protein-ligand 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 | ![]() ![]() | ||||||
![]() | Stengl, B. / Meyer, E.A. / Heine, A. / Brenk, R. / Diederich, F. / Klebe, G. | ||||||
![]() | ![]() Title: Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding. Authors: Stengl, B. / Meyer, E.A. / Heine, A. / Brenk, R. / Diederich, F. / Klebe, G. #1: ![]() Title: Synthesis, biological evaluation and crystallographic studies of extended guanine-based (lin-benzoguanine) inhibitors for tRNA-guanine transglycosylase (TGT) Authors: Meyer, E.A. / Donati, N. / Guillot, M. / Schweizer, B. / Diederich, F. / Stengl, B. / Heine, A. / Brenk, R. / Klebe, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 94.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 69.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 451.7 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1y5vC ![]() 1y5wC ![]() 1y5xC ![]() 1pudS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 42925.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: GenBank: 11095422, UniProt: P28720*PLUS, tRNA-guanosine34 preQ1 transglycosylase |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-344 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.12 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 8000, MES, DMSO, DTT, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 6, 2002 / Details: MIRRORS |
Radiation | Monochromator: YALE MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 44525 / % possible obs: 98.7 % / Rsym value: 0.043 |
Reflection shell | Resolution: 1.7→1.73 Å / Rsym value: 0.0167 / % possible all: 99.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PUD Resolution: 1.7→32.8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 662304.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.6745 Å2 / ksol: 0.359238 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→32.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|