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Yorodumi- PDB-3hy0: Crystal Structure of catalytic fragment of E. coli AlaRS G237A in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hy0 | ||||||
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Title | Crystal Structure of catalytic fragment of E. coli AlaRS G237A in complex with GlySA | ||||||
Components | Alanyl-tRNA synthetaseAlanine—tRNA ligase | ||||||
Keywords | LIGASE / Aminoacyl-tRNA synthetase / Protein biosynthesis / Nucleotide-binding / amino acid-binding / ATP-binding / Metal-binding / Zinc-finger | ||||||
Function / homology | Function and homology information Ser-tRNA(Ala) hydrolase activity / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / DNA-binding transcription repressor activity / tRNA binding / negative regulation of DNA-templated transcription / protein homodimerization activity / zinc ion binding ...Ser-tRNA(Ala) hydrolase activity / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / DNA-binding transcription repressor activity / tRNA binding / negative regulation of DNA-templated transcription / protein homodimerization activity / zinc ion binding / ATP binding / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Guo, M. / Yang, X.-L. / Schimmel, P. | ||||||
Citation | Journal: Nature / Year: 2009 Title: Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma. Authors: Guo, M. / Chong, Y.E. / Shapiro, R. / Beebe, K. / Yang, X.L. / Schimmel, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hy0.cif.gz | 220.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hy0.ent.gz | 173.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/3hy0 ftp://data.pdbj.org/pub/pdb/validation_reports/hy/3hy0 | HTTPS FTP |
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-Related structure data
Related structure data | 3hxuC 3hxvC 3hxwC 3hxxC 3hxyC 3hxzC 3hy1C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49938.082 Da / Num. of mol.: 2 / Fragment: N-terminal Catalytic fragment residues 2-442 / Mutation: H104L, Q108L, E112L, G237A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: alaS, lovB, b2697, JW2667 / Plasmid: pET20b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CondonPlus / References: UniProt: P00957, alanine-tRNA ligase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-HED / #5: 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: 4.15 Å3/Da / Density % sol: 70.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 32% PEG400, 0.1 M HEPES, pH 7.8, vapor diffusion, sitting drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97971 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97971 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 131348 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 19.509 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.79 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.179 / SU ML: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→39.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å
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