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Yorodumi- PDB-1n2v: Crystal Structure of TGT in complex with 2-Butyl-5,6-dihydro-1H-i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n2v | ||||||
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Title | Crystal Structure of TGT in complex with 2-Butyl-5,6-dihydro-1H-imidazo[4,5-d]pyridazine-4,7-dione | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE / Protein-Ligand complex | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Brenk, R. / Naerum, L. / Graedler, U. / Gerber, H.-D. / Garcia, G.A. / Reuter, K. / Stubbs, M.T. / Klebe, G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2003 Title: Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis Authors: Brenk, R. / Naerum, L. / Graedler, U. / Gerber, H.-D. / Garcia, G.A. / Reuter, K. / Stubbs, M.T. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n2v.cif.gz | 91.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n2v.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 1n2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/1n2v ftp://data.pdbj.org/pub/pdb/validation_reports/n2/1n2v | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-BDI / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.75 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, Tris, DMSO, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 395K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7.5 Details: Romier, C., (1996) Proteins: Struct.,Funct., Genet., 24, 516. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 28, 2000 / 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: 2.1→30 Å / Num. all: 23882 / Num. obs: 23842 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rsym value: 0.095 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 99.4 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 23882 / Num. measured all: 87053 / Rmerge(I) obs: 0.095 |
Reflection shell | *PLUS % possible obs: 99.4 % / Rmerge(I) obs: 0.302 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.12 Å /
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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