+Open data
-Basic information
Entry | Database: PDB / ID: 4hjr | ||||||
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Title | Crystal structure of F2YRS | ||||||
Components | Tyrosine-tRNA ligaseTyrosine—tRNA ligase | ||||||
Keywords | LIGASE / AMINOACYL-TRNA SYNTHETASE / F2Y | ||||||
Function / homology | Function and homology information tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii DSM 2661 (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wang, J. / Tian, C. / Gong, W. / Li, F. / Shi, P. / Li, J. / Ding, W. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2013 Title: A genetically encoded 19F NMR probe for tyrosine phosphorylation. Authors: Li, F. / Shi, P. / Li, J. / Yang, F. / Wang, T. / Zhang, W. / Gao, F. / Ding, W. / Li, D. / Li, J. / Xiong, Y. / Sun, J. / Gong, W. / Tian, C. / Wang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hjr.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hjr.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 4hjr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/4hjr ftp://data.pdbj.org/pub/pdb/validation_reports/hj/4hjr | HTTPS FTP |
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-Related structure data
Related structure data | 4hjxC 1j1uS 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
#1: Protein | Mass: 36051.777 Da / Num. of mol.: 2 / Mutation: Y32R,L65Y,H70G,F108N,Q109C,D158N,L162S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: tyrS, MJ0389 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57834, tyrosine-tRNA ligase #2: 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: 2.15 Å3/Da / Density % sol: 42.87 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 50 mM Tris, pH 7.5, 500 mM NaCl, 10 mM -mercaptoethanol,VAPOR DIFFUSION, SITTING DROP, temperature 289K, temperature 289.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 21238 / Num. obs: 20580 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 18.98 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.97 / Num. unique all: 1969 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J1U Resolution: 2.5→29.729 Å / SU ML: 0.41 / σ(F): 0.35 / Phase error: 34.94 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.729 Å
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Refine LS restraints |
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LS refinement shell |
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