[English] 日本語
Yorodumi- PDB-5i02: tRNA guanine transglycosylase (TGT) in co-crystallized complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i02 | ||||||
---|---|---|---|---|---|---|---|
Title | tRNA guanine transglycosylase (TGT) in co-crystallized complex with 6-amino-4-{2-[(cyclohexylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE / co-crystallization / shigellosis / TRANSFERASE INHIBITOR | ||||||
Function / homology | Function and homology information tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Zymomonas mobilis subsp. mobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Ehrmann, F.R. / Nguyen, D. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To be Published Title: Co-crystallization, Isothermal titration calorimetry and nanoESI-MS reveal dimer disturbing inhibitors Authors: Ehrmann, F.R. / Stojko, J. / Heine, A. / Diederich, F. / Reuter, K. / Sanglier-Cianferani, S. / Klebe, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5i02.cif.gz | 172.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5i02.ent.gz | 135.2 KB | Display | PDB format |
PDBx/mmJSON format | 5i02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/5i02 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/5i02 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5i00C 5i03C 5i06C 5i07C 5i09C 1p0dS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42838.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria) Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
---|
-Non-polymers , 6 types, 325 molecules
#2: Chemical | ChemComp-ZN / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-PK2 / | ||||||
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.69 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→42.53 Å / Num. obs: 105188 / % possible obs: 99.1 % / Redundancy: 3.3 % / Rsym value: 0.055 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.25→1.33 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.1 / % possible all: 97.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P0D Resolution: 1.25→42.152 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.71
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→42.152 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|