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Yorodumi- PDB-1h3f: Tyrosyl-tRNA synthetase from Thermus thermophilus complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h3f | ||||||
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Title | Tyrosyl-tRNA synthetase from Thermus thermophilus complexed with tyrosinol | ||||||
Components | TYROSYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / AMINOACYL-TRNA SYNTHETASE / ATP + L-TYROSINE + TRNA(TYR)->AMP + PPI + L-TYROSYL-TRNA(TY CLASS I AMINOACYL-TRNA SYNTHETASE | ||||||
Function / homology | Function and homology information tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Cusack, S. / Yaremchuk, A. / Kriklivyi, I. / Tukalo, M. | ||||||
Citation | Journal: Embo J. / Year: 2002 Title: Class I Tyrosyl-tRNA Synthetase Has a Class II Mode or tRNA Recognition Authors: Yaremchuk, A. / Kriklivyi, I. / Tukalo, M. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h3f.cif.gz | 171.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h3f.ent.gz | 142.9 KB | Display | PDB format |
PDBx/mmJSON format | 1h3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/1h3f ftp://data.pdbj.org/pub/pdb/validation_reports/h3/1h3f | 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 48786.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P83453, tyrosine-tRNA ligase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY: ATP + L-TYROSINE + TRNA(TYR) = AMP + DIPHOSPHATE + L-TYROSYL-TRNA(TYR). ...CATALYTIC ACTIVITY: ATP + L-TYROSINE + TRNA(TYR) = AMP + DIPHOSPHAT | Sequence details | UNMODELLED | |
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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: 2.7 Å3/Da / Density % sol: 54.6 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 Details: 12MG/ML PROTEIN IN 1:1 RATIO WITH RESERVOIR SOLUTION CONTAINING 1.2M AMMONIUM SULPHATE, 50MM MES(PH5.8), 10MM MGCL2, 0.5MM DDT, pH 5.80 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 70951 / % possible obs: 97.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.3 / % possible all: 84.5 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 464280 |
Reflection shell | *PLUS % possible obs: 84.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: T. THERMOPHILUS TYROSYL-TRNA SYNTHETASE PREVIOUSLY DETERMINED BY SIRAS BY SAME AUTHORS Resolution: 2→25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1834546.75 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: CHAIN A RESIDUES 1-4, 80-100 AND 348-351 AND CHAIN B RESIDUES 1-4, 84-96 AND 345-352 WERE UNMODELED DUE TO DISORDER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.6936 Å2 / ksol: 0.38785 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection Rfree: 3557 / % reflection Rfree: 4.9 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.233 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.28 |