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Yorodumi- PDB-3l4g: Crystal structure of Homo Sapiens cytoplasmic Phenylalanyl-tRNA s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l4g | ||||||
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Title | Crystal structure of Homo Sapiens cytoplasmic Phenylalanyl-tRNA synthetase | ||||||
Components |
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Keywords | LIGASE / aminoacylation / tRNA-binding / DNA-binding domain / four-helix bundle / Acetylation / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Nucleotide-binding / Phosphoprotein / Polymorphism / Protein biosynthesis | ||||||
Function / homology | Function and homology information phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / protein heterotetramerization / tRNA binding / translation / magnesium ion binding ...phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / protein heterotetramerization / tRNA binding / translation / magnesium ion binding / RNA binding / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Finarov, I. / Moor, N. / Kessler, N. / Klipcan, L. / Safro, M.G. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns. Authors: Finarov, I. / Moor, N. / Kessler, N. / Klipcan, L. / Safro, M.G. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Crystallization and X-ray analysis of human cytoplasmic phenylalanyl-tRNA synthetase Authors: Finarov, I. / Moor, N. / Kessler, N. / Safro, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l4g.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3l4g.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 3l4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/3l4g ftp://data.pdbj.org/pub/pdb/validation_reports/l4/3l4g | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 57644.527 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FARSA, FARS, FARSL, FARSLA / Plasmid: Pet21 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: Q9Y285, phenylalanine-tRNA ligase #2: Protein | Mass: 66214.484 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FARSB, FARSLB, FRSB, HSPC173 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: Q9NSD9, phenylalanine-tRNA ligase #3: Chemical | ChemComp-PHE / |
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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: 3.41 Å3/Da / Density % sol: 63.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 1.04M NaCitrate, MES pH 6.4, 5mM 2-mercaptoethanol, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. all: 199279 / Num. obs: 193345 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.24 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PYS and 2CXI Resolution: 3.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 1778 / Stereochemistry target values: Engh & Huber Details: a non-crystallographic symmetry for most parts of the molecules in assymetric unit was used
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Solvent computation | Bsol: 105.879 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 120.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→30 Å
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Refine LS restraints |
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LS refinement shell |
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