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Yorodumi- PDB-1q66: CRYSTAL STRUCTURE OF TGT IN COMPLEX WITH 2-AMINO-6-AMINOMETHYL-8-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q66 | ||||||
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Title | CRYSTAL STRUCTURE OF TGT IN COMPLEX WITH 2-AMINO-6-AMINOMETHYL-8-phenylsulfanylmethyl-3H-QUINAZOLIN-4-ONE crystallized at pH 5.5 | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
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: 1.75 Å | ||||||
Authors | Brenk, R. / Meyer, E. / Reuter, K. / Stubbs, M.T. / Garcia, G.A. / Klebe, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystallographic Study of Inhibitors of tRNA-guanine Transglycosylase Suggests a New Structure-based Pharmacophore for Virtual Screening. Authors: Brenk, R. / Meyer, E. / Reuter, K. / Stubbs, M.T. / Garcia, G.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 | 1q66.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q66.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/1q66 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/1q66 | HTTPS FTP |
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-Related structure data
Related structure data | 1q4wC 1q63C 1q65C 1r5yC 1pudS S: Starting model for refinement C: citing same article (ref.) |
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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-KMB / |
#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: 2.41 Å3/Da / Density % sol: 48.89 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 8000, TRIS, DMSO, DTT, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 30, 2001 / 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: 1.75→40 Å / Num. obs: 38581 / % possible obs: 93.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.043 |
Reflection shell | Resolution: 1.75→1.83 Å / Rsym value: 0.213 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1PUD Resolution: 1.75→40 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 646321.68 / Data cutoff high rms absF: 646321.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.5707 Å2 / ksol: 0.376215 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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