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Yorodumi- PDB-2ag6: Crystal structure of p-bromo-l-phenylalanine-tRNA sythetase in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ag6 | ||||||
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Title | Crystal structure of p-bromo-l-phenylalanine-tRNA sythetase in complex with p-bromo-l-phenylalanine | ||||||
Components | Tyrosyl-tRNA synthetase | ||||||
Keywords | LIGASE / Structural plasticity / Unnatural amino acid / tRNA Synthetase / Bromo-phenylalanine | ||||||
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 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Turner, J.M. / Graziano, J. / Spraggon, G. / Schultz, P.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Structural plasticity of an aminoacyl-tRNA synthetase active site Authors: Turner, J.M. / Graziano, J. / Spraggon, G. / Schultz, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ag6.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ag6.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ag6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/2ag6 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/2ag6 | HTTPS FTP |
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-Related structure data
Related structure data | 1zh0C 1zh6S 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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Unit cell |
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-Components
#1: Protein | Mass: 36079.887 Da / Num. of mol.: 1 / Mutation: Y32L, E107S,D158P,I159L,L162E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: tyrS / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57834, tyrosine-tRNA ligase |
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#2: Chemical | ChemComp-4BF / |
#3: 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: 2.7 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG-300, %% PEG-8000, 10% GLYCEROL, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→80 Å / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 39.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 4.75 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB Entry 1ZH6 Resolution: 1.9→72.55 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.399 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.762 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→72.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 80.2868 Å / Origin y: 41.6923 Å / Origin z: 4.777 Å
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