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Yorodumi- PDB-7fg6: Crystal structure of the Tyrosyl-tRNA synthetase (TyrRS) in Nanoa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fg6 | ||||||
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Title | Crystal structure of the Tyrosyl-tRNA synthetase (TyrRS) in Nanoarchaeum equitans | ||||||
Components | Tyrosine--tRNA ligase | ||||||
Keywords | LIGASE / TyrRS / tRNA synthetase | ||||||
Function / homology | Function and homology information tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Nanoarchaeum equitans Kin4-M (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Noguchi, H. / Kamata, K. / Park, S.Y. / Tamura, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: Crystal structure of Nanoarchaeum equitans tyrosyl-tRNA synthetase and its aminoacylation activity toward tRNA Tyr with an extra guanosine residue at the 5'-terminus. Authors: Horikoshi, T. / Noguchi, H. / Umehara, T. / Mutsuro-Aoki, H. / Kurihara, R. / Noguchi, R. / Hashimoto, T. / Watanabe, Y. / Ando, T. / Kamata, K. / Park, S.Y. / Tamura, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fg6.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fg6.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 7fg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/7fg6 ftp://data.pdbj.org/pub/pdb/validation_reports/fg/7fg6 | HTTPS FTP |
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-Related structure data
Related structure data | 1j1uS 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
#1: Protein | Mass: 43244.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nanoarchaeum equitans Kin4-M (archaea) / Strain: Kin4-M / Gene: tyrS / Production host: Escherichia coli (E. coli) / References: UniProt: Q74MD3, tyrosine-tRNA ligase |
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#2: 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: 2.53 Å3/Da / Density % sol: 51.41 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Magnesium acetate, 0.1 M Sodium cacodylate pH6.5, 20% (w/v) PEG 8,000 |
-Data collection
Diffraction | Mean temperature: 93.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→45.59 Å / Num. obs: 11299 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 63.73 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.072 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 10.6 % / Num. unique obs: 1606 / CC1/2: 0.69 / Rpim(I) all: 0.566 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1j1u Resolution: 2.8→45.59 Å / SU ML: 0.4082 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.2755 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.66 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→45.59 Å
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Refine LS restraints |
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LS refinement shell |
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