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Yorodumi- PDB-3eos: tRNA-guanine transglycosylase in complex with 6-amino-4-{2-[(cycl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eos | ||||||
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Title | tRNA-guanine transglycosylase in 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 / TIM Barrel / Glycosyltransferase / Metal-binding / Queuosine biosynthesis / tRNA processing | ||||||
Function / homology | Function and homology information 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 | Zymomonas mobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / AB INITIO / Resolution: 1.78 Å | ||||||
Authors | Ritschel, T. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Chemmedchem / Year: 2009 Title: How to Replace the Residual Solvation Shell of Polar Active Site Residues to Achieve Nanomolar Inhibition of tRNA-Guanine Transglycosylase Authors: Ritschel, T. / Kohler, P.C. / Neudert, G. / Heine, A. / Diederich, F. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eos.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eos.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 3eos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/3eos ftp://data.pdbj.org/pub/pdb/validation_reports/eo/3eos | HTTPS FTP |
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-Related structure data
Related structure data | 3eouC 3gc4C 3gc5C 3ge7C 1p0eS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Zymomonas mobilis (bacteria) / Gene: tgt / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | ChemComp-PK2 / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | 312TH RESIDUE IS LYS ACCORDING TO REUTER K.K.H. ET AL [J. BACTERIOL. 177:5284-5288(1995)] AND AHN J. ...312TH RESIDUE IS LYS ACCORDING TO REUTER K.K.H. ET AL [J. BACTERIOL. 177:5284-5288(1995)] AND AHN J.Y. ET AL [SUBMITTED (OCT-2000) TO THE EMBL/GENBANK/DDBJ DATABASES] | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.9 % |
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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 |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 30, 2008 / Details: Mirror |
Radiation | Monochromator: Yale Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→30 Å / Num. all: 38665 / Num. obs: 38665 / % possible obs: 98.9 % / Redundancy: 2.6 % / Rsym value: 0.06 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1752 / Rsym value: 0.39 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB ENTRY 1P0E Resolution: 1.78→10 Å / Num. parameters: 12144 / Num. restraintsaints: 11522 / Cross valid method: FREE R / σ(F): 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
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 2663 / Occupancy sum non hydrogen: 3003.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→10 Å
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Refine LS restraints |
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