+Open data
-Basic information
Entry | Database: PDB / ID: 4hjx | ||||||
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Title | Crystal structure of F2YRS complexed with F2Y | ||||||
Components | Tyrosine-tRNA ligase | ||||||
Keywords | LIGASE / AMINOACYL-TRNA SYNTHETASE | ||||||
Function / homology | Function and homology information tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanococcus Jannaschii DSM 2661 (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.91 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 | 4hjx.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hjx.ent.gz | 104.1 KB | Display | PDB format |
PDBx/mmJSON format | 4hjx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hjx_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 4hjx_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 4hjx_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 4hjx_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/4hjx ftp://data.pdbj.org/pub/pdb/validation_reports/hj/4hjx | HTTPS FTP |
-Related structure data
Related structure data | 4hjrC 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.) Methanococcus 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 #2: Chemical | #3: 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: 2.55 Å3/Da / Density % sol: 51.84 % |
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-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 Satun 944 HG / Detector: CCD / Date: Aug 23, 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: 2.91→50 Å / Num. all: 16153 / Num. obs: 16105 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.91→3.01 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1601 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J1U Resolution: 2.91→24.594 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 28.67 / 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: 2.91→24.594 Å
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Refine LS restraints |
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LS refinement shell |
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