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Yorodumi- PDB-1iq8: Crystal Structure of archaeosine tRNA-guanine transglycosylase fr... -
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-Basic information
Entry | Database: PDB / ID: 1iq8 | ||||||
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Title | Crystal Structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii | ||||||
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 / MAD / Resolution: 2.2 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 | 1iq8.cif.gz | 240.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iq8.ent.gz | 194.5 KB | Display | PDB format |
PDBx/mmJSON format | 1iq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/1iq8 ftp://data.pdbj.org/pub/pdb/validation_reports/iq/1iq8 | HTTPS FTP |
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-Related 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: 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: 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: 3.36 Å3/Da / Density % sol: 63.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: sodium phosphate, potassium phosphate, sodium 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: BL44XU / Wavelength: 0.9 Å |
Detector | Type: OXFORD PX210 / Detector: CCD / Date: Nov 20, 2000 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 530165 / Num. obs: 530165 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 34 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 7.1 / Num. unique all: 4241 / Rsym value: 0.256 / % possible all: 93 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 88967 / Num. measured all: 530165 / Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS % possible obs: 93 % / Num. unique obs: 4241 / Num. measured obs: 17411 / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 7.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→50 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 40.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor obs: 0.227 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.227 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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