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Yorodumi- PDB-2quk: Crystal structures of human tryptophanyl-tRNA synthetase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2quk | ||||||
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Title | Crystal structures of human tryptophanyl-tRNA synthetase in complex with ATP(putative) | ||||||
Components | Tryptophanyl-tRNA synthetase | ||||||
Keywords | LIGASE / aminoacyl-tRNA synthetase / Rossmann fold / induced-fit mechnism / ATP-binding / Cytoplasm / Nucleotide-binding / Protein biosynthesis | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / angiogenesis / translation ...tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / angiogenesis / translation / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of gene expression / protein kinase binding / protein homodimerization activity / protein-containing complex / extracellular exosome / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Shen, N. / Ding, J.P. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2008 Title: Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states Authors: Shen, N. / Zhou, M. / Yang, B. / Yu, Y. / Dong, X. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2quk.cif.gz | 90.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2quk.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 2quk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2quk_validation.pdf.gz | 432.6 KB | Display | wwPDB validaton report |
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Full document | 2quk_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 2quk_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2quk_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/2quk ftp://data.pdbj.org/pub/pdb/validation_reports/qu/2quk | HTTPS FTP |
-Related structure data
Related structure data | 2quhC 2quiC 2qujC 1o5tS 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
#1: Protein | Mass: 54060.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WARS, IFI53, WRS / Plasmid: pET24a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23381, tryptophan-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: 3.62 Å3/Da / Density % sol: 65.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: PEG3350, PEG1500, Na Citrate,, pH8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
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→50 Å / Num. obs: 20030 / % possible obs: 99.1 % / Redundancy: 7.6 % / Biso Wilson estimate: 50.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.8→2.93 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.6 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O5T Resolution: 2.8→50 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3596708.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.1018 Å2 / ksol: 0.346341 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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