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- PDB-3kt8: Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kt8 | ||||||
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Title | Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with L-tryptophanamide | ||||||
![]() | Tryptophanyl-tRNA synthetase, cytoplasmic | ||||||
![]() | LIGASE / tryptophanyl-tRNA synthetase / S. cerevisiae / sulfate ion / amino acid activation / catalytic mechanism / tryptophanamide / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Nucleotide-binding / Protein biosynthesis | ||||||
Function / homology | ![]() tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, M. / Dong, X. / Zhong, C. / Shen, N. / Ding, J. | ||||||
![]() | ![]() Title: Crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase: new insights into the mechanism of tryptophan activation and implications for anti-fungal drug design Authors: Zhou, M. / Dong, X. / Shen, N. / Zhong, C. / Ding, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 319.2 KB | Display | ![]() |
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PDB format | ![]() | 262.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.8 KB | Display | ![]() |
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Full document | ![]() | 501.5 KB | Display | |
Data in XML | ![]() | 53.7 KB | Display | |
Data in CIF | ![]() | 72.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3kt0SC ![]() 3kt3C ![]() 3kt6C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50248.094 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: trpS / Plasmid: pET3E / Production host: ![]() ![]() #2: Chemical | ChemComp-LTN / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.089597 Å3/Da / Density % sol: 75.833054 % / Mosaicity: 0.757 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.1M HEPES, 2.2M (NH4)2SO4, pH 5.9, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 23, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 79287 / % possible obs: 97.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.117 / Χ2: 1.604 / Net I/σ(I): 11.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3KT0 Resolution: 3→49.04 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 0.65 / SU B: 15.77 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.585 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 193.48 Å2 / Biso mean: 80.62 Å2 / Biso min: 36.08 Å2
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Refinement step | Cycle: LAST / Resolution: 3→49.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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