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Yorodumi- PDB-3kt3: Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kt3 | ||||||
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Title | Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with TrpAMP | ||||||
Components | Tryptophanyl-tRNA synthetase, cytoplasmic | ||||||
Keywords | LIGASE / tryptophanyl-tRNA synthetase / S. cerevisiae / sulfate ion / amino acid activation / catalytic mechanism / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Nucleotide-binding / Protein biosynthesis | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / sequence-specific mRNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Zhou, M. / Dong, X. / Zhong, C. / Shen, N. / Ding, J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kt3.cif.gz | 624.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kt3.ent.gz | 519 KB | Display | PDB format |
PDBx/mmJSON format | 3kt3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kt3_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3kt3_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3kt3_validation.xml.gz | 57.8 KB | Display | |
Data in CIF | 3kt3_validation.cif.gz | 78 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/3kt3 ftp://data.pdbj.org/pub/pdb/validation_reports/kt/3kt3 | HTTPS FTP |
-Related structure data
Related structure data | 3kt0SC 3kt6C 3kt8C 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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2 |
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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.) Saccharomyces cerevisiae (brewer's yeast) Gene: trpS / Plasmid: pET3E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12109, tryptophan-tRNA ligase #2: Chemical | ChemComp-TYM / #3: Chemical | ChemComp-SO4 / #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: 5.056929 Å3/Da / Density % sol: 75.676941 % / Mosaicity: 0.608 ° |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.6→50 Å / Num. obs: 118348 / % possible obs: 96.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.056 / Χ2: 0.94 / Net I/σ(I): 22.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KT0 Resolution: 2.6→48.94 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.8 / SU B: 17.308 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.22 / 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: 150.02 Å2 / Biso mean: 53.4 Å2 / Biso min: 26.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→48.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.602→2.669 Å / Total num. of bins used: 20
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