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Yorodumi- PDB-4q93: Crystal structure of resveratrol bound human tyrosyl tRNA synthetase -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q93 | ||||||
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Title | Crystal structure of resveratrol bound human tyrosyl tRNA synthetase | ||||||
Components | Tyrosine--tRNA ligase, cytoplasmic | ||||||
Keywords | LIGASE / Resveratrol / Aminoacyl tRNA synthetases / Amino acid activation / active site | ||||||
Function / homology | Function and homology information interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process ...interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process / extracellular space / RNA binding / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Mathew, S. / Schimmel, P. | ||||||
Citation | Journal: Nature / Year: 2014 Title: A human tRNA synthetase is a potent PARP1-activating effector target for resveratrol. Authors: Sajish, M. / Schimmel, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q93.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q93.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 4q93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/4q93 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/4q93 | HTTPS FTP |
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-Related structure data
Related structure data | 4qbtC 1n3lS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42133.559 Da / Num. of mol.: 1 / Fragment: mini TyrRS (UNP residues 1-364) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YARS / Production host: Escherichia coli (E. coli) / References: UniProt: P54577, tyrosine-tRNA ligase |
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-Non-polymers , 6 types, 241 molecules
#2: Chemical | ChemComp-STL / | ||||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Chemical | #7: 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: 2.5 Å3/Da / Density % sol: 50.76 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.1 M ammonium sulfate, 0.1 M sodium phosphate monobasic / potassium phosphate dibasic, pH 6-8, 2% acetone, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 1, 2012 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 25654 / Num. obs: 25438 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1161 / Rsym value: 0.271 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N3L Resolution: 2.1→37.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.867 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.184 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.664 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→37.01 Å
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Refine LS restraints |
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