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Yorodumi- PDB-6kid: Crystal structure of human leucyl-tRNA synthetase, ATP-bound form -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kid | ||||||
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Title | Crystal structure of human leucyl-tRNA synthetase, ATP-bound form | ||||||
Components | Leucine--tRNA ligase, cytoplasmic | ||||||
Keywords | LIGASE / leucyl-tRNA synthetase / ATP-bound structure | ||||||
Function / homology | Function and homology information glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / Selenoamino acid metabolism / leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / cellular response to leucine starvation / Cytosolic tRNA aminoacylation / cellular response to L-leucine / aminoacyl-tRNA synthetase multienzyme complex ...glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / Selenoamino acid metabolism / leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / cellular response to leucine starvation / Cytosolic tRNA aminoacylation / cellular response to L-leucine / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / regulation of cell size / positive regulation of TOR signaling / endomembrane system / positive regulation of TORC1 signaling / cellular response to amino acid starvation / GTPase activator activity / cellular response to amino acid stimulus / positive regulation of GTPase activity / lysosome / nuclear body / endoplasmic reticulum / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Kim, S. / Son, J. / Kim, S. / Hwang, K.Y. | ||||||
Citation | Journal: Cell Rep / Year: 2021 Title: Leucine-sensing mechanism of leucyl-tRNA synthetase 1 for mTORC1 activation. Authors: Kim, S. / Yoon, I. / Son, J. / Park, J. / Kim, K. / Lee, J.H. / Park, S.Y. / Kang, B.S. / Han, J.M. / Hwang, K.Y. / Kim, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kid.cif.gz | 433 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kid.ent.gz | 345.9 KB | Display | PDB format |
PDBx/mmJSON format | 6kid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/6kid ftp://data.pdbj.org/pub/pdb/validation_reports/ki/6kid | HTTPS FTP |
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-Related structure data
Related structure data | 6kieC 6kqyC 6kr7C 1wz2S 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: 136055.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: LARS, KIAA1352 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P2J5, leucine-tRNA ligase | ||||
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#2: Chemical | ChemComp-ATP / | ||||
#3: Chemical | ChemComp-LEU / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.37 Å3/Da / Density % sol: 71.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES (pH 7.1), 0.42 M Ammonium sulfate, 24 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 273 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Apr 12, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.96→50 Å / Num. obs: 82644 / % possible obs: 88.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.106 / Rrim(I) all: 0.202 / Χ2: 1.336 / Net I/σ(I): 5 / Num. measured all: 230992 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1wz2 Resolution: 3.15→42.89 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 27.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.52 Å2 / Biso mean: 46.754 Å2 / Biso min: 12.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.15→42.89 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
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