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Yorodumi- PDB-1pxg: Crystal structure of the mutated tRNA-guanine transglycosylase (T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pxg | ||||||
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Title | Crystal structure of the mutated tRNA-guanine transglycosylase (TGT) D280E complexed with preQ1 | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE / TIM-barrel | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kittendorf, J.D. / Sgraja, T. / Reuter, K. / Klebe, G. / Garcia, G.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: An essential role for aspartate 264 in catalysis by tRNA-guanine transglycosylase from Escherichia coli. Authors: Kittendorf, J.D. / Sgraja, T. / Reuter, K. / Klebe, G. / Garcia, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pxg.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pxg.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/1pxg ftp://data.pdbj.org/pub/pdb/validation_reports/px/1pxg | HTTPS FTP |
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-Related structure data
Related structure data | 1pudS 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: 42450.156 Da / Num. of mol.: 1 / Mutation: D280E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: TGT / Plasmid: pETZM4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-PRF / | ||
#4: Chemical | ChemComp-GOL / #5: 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: 2.16 Å3/Da / Density % sol: 49.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, dimethylsulfoxide, tris hydrochloride, DTT, preQ1, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25. ℃ / pH: 7.5 / Method: vapor diffusion, hanging dropDetails: Romier, C., (1996) Proteins: Struct.,Funct., Genet., 24, 516. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 6, 2002 / Details: osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 42492 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 6.1 / Num. unique all: 42492 / Rsym value: 0.253 / % possible all: 90.6 |
Reflection | *PLUS Num. measured all: 155496 |
Reflection shell | *PLUS % possible obs: 90.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1PUD Resolution: 1.7→10 Å / Num. parameters: 12823 / Num. restraintsaints: 11936 / 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
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Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 2736.99 / Occupancy sum non hydrogen: 3169.49 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 3 % / Rfactor Rwork: 0.159 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |