[English] 日本語
![](img/lk-miru.gif)
- PDB-3rr4: tRNA-Guanine Transglycosylase in complex with N-Methyl-lin-Benzog... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3rr4 | ||||||
---|---|---|---|---|---|---|---|
Title | tRNA-Guanine Transglycosylase in complex with N-Methyl-lin-Benzoguanine Inhibitor | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | Transferase/transferase inhibitor / TIM BARREL / GLYCOSYLTRANSFERASE / METAL-BINDING / QUEUOSINE / BIOSYNTHESIS / TRANSFERASE / TRNA PROCESSING / TRNA / 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 | ![]() ![]() | ||||||
![]() | Klebe, G. / Immekus, F. / Heine, A. | ||||||
![]() | ![]() Title: From lin-Benzoguanines to lin-Benzohypoxanthines as Ligands for Zymomonas mobilis tRNA-Guanine Transglycosylase: Replacement of Protein-Ligand Hydrogen Bonding by Importing Water Clusters. Authors: Barandun, L.J. / Immekus, F. / Kohler, P.C. / Tonazzi, S. / Wagner, B. / Wendelspiess, S. / Ritschel, T. / Heine, A. / Kansy, M. / Klebe, G. / Diederich, F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 94.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 450.8 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3s1gC ![]() 3sm0C ![]() 3tllC ![]() 1p0dS ![]() 3gfn C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 42925.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||
---|---|---|---|
#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-HRD / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 48.67 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100MM TRIS HCL, 1MM DTT, 10% DMSO, 5% PEG 8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 26, 2010 / Details: Rh-coated silicon with indirect water cooling |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→30 Å / Num. all: 45107 / Num. obs: 45107 / % possible obs: 96.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 0.059 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2115 / Rsym value: 0.287 / % possible all: 90.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO PHASING Starting model: pdb entry 1P0D Resolution: 1.68→30 Å / Num. parameters: 12753 / Num. restraintsaints: 12104 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 2745.95 / Occupancy sum non hydrogen: 3119.54 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→30 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|