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Yorodumi- PDB-5thl: Crystal structure of the human tyrosyl-tRNA synthetase mutant G41R -
+Open data
-Basic information
Entry | Database: PDB / ID: 5thl | ||||||
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Title | Crystal structure of the human tyrosyl-tRNA synthetase mutant G41R | ||||||
Components | Tyrosine--tRNA ligase, cytoplasmic | ||||||
Keywords | LIGASE / Tyrosyl-tRNA synthetase / CMT / mutant | ||||||
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 / RNA binding / extracellular space / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Blocquel, D. / Sajish, M. / Yang, X.L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Alternative stable conformation capable of protein misinteraction links tRNA synthetase to peripheral neuropathy. Authors: Blocquel, D. / Li, S. / Wei, N. / Daub, H. / Sajish, M. / Erfurth, M.L. / Kooi, G. / Zhou, J. / Bai, G. / Schimmel, P. / Jordanova, A. / Yang, X.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5thl.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5thl.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 5thl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5thl_validation.pdf.gz | 425 KB | Display | wwPDB validaton report |
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Full document | 5thl_full_validation.pdf.gz | 429.6 KB | Display | |
Data in XML | 5thl_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 5thl_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/5thl ftp://data.pdbj.org/pub/pdb/validation_reports/th/5thl | HTTPS FTP |
-Related structure data
Related structure data | 5thhC 1n3lS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 42233.699 Da / Num. of mol.: 1 / Mutation: G41R 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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#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: 2.53 Å3/Da / Density % sol: 51.35 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / Details: ammonium sulfate, acetone, sodium phosphate |
-Data collection
Diffraction | Mean temperature: 193 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 57743 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.077 / Χ2: 2.018 / Net I/av σ(I): 39.789 / Net I/σ(I): 11.4 / Num. measured all: 392235 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N3L Resolution: 1.6→31.989 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 0 / Phase error: 19.18
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 37.304 Å2 / ksol: 0.382 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 71.87 Å2 / Biso mean: 24.9432 Å2 / Biso min: 10.33 Å2
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Refinement step | Cycle: final / Resolution: 1.6→31.989 Å
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