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Yorodumi- PDB-1it8: Crystal structure of archaeosine tRNA-guanine transglycosylase fr... -
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-Basic information
Entry | Database: PDB / ID: 1it8 | ||||||
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Title | Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0 | ||||||
Components | archaeosine tRNA-guanine transglycosylase | ||||||
Keywords | TRANSFERASE / (alpha/beta)8 barrel / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information tRNA-guanine15 transglycosylase / pentosyltransferase activity / tRNA modification / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ishitani, R. / Nureki, O. / Fukai, S. / Kijimoto, T. / Nameki, N. / Watanabe, M. / Kondo, H. / Sekine, M. / Okada, N. / Nishimura, S. ...Ishitani, R. / Nureki, O. / Fukai, S. / Kijimoto, T. / Nameki, N. / Watanabe, M. / Kondo, H. / Sekine, M. / Okada, N. / Nishimura, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structure of archaeosine tRNA-guanine transglycosylase. Authors: Ishitani, R. / Nureki, O. / Fukai, S. / Kijimoto, T. / Nameki, N. / Watanabe, M. / Kondo, H. / Sekine, M. / Okada, N. / Nishimura, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1it8.cif.gz | 239.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1it8.ent.gz | 193 KB | Display | PDB format |
PDBx/mmJSON format | 1it8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/1it8 ftp://data.pdbj.org/pub/pdb/validation_reports/it/1it8 | HTTPS FTP |
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-Related structure data
Related structure data | 1iq8SC 1it7C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 66700.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O58843, tRNA-guanosine34 preQ1 transglycosylase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PQ0 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Na phosphate, K phosphate, Na acetate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal grow | *PLUS Details: Ishitani, R., (2001) Acta Cryst., D57, 1659. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.02 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 19, 2002 / Details: mirrors |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 282730 / Num. obs: 282730 / % possible obs: 96 % / Redundancy: 4.5 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 8.69 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 2.14 / Num. unique all: 2975 / Rsym value: 0.202 / % possible all: 92.3 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 63242 / Num. measured all: 282730 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 92.3 % / Num. unique obs: 2975 / Num. measured obs: 8560 / Rmerge(I) obs: 0.202 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IQ8 Resolution: 2.5→34.87 Å / Rfactor Rfree error: 0.003 / 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: 24.2285 Å2 / ksol: 0.336052 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→34.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Rfactor obs: 0.2315 / Rfactor Rfree: 0.2785 / Rfactor Rwork: 0.2315 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.381 / Rfactor Rwork: 0.355 / Rfactor obs: 0.355 |