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Yorodumi- PDB-3hy1: Crystal Structure of catalytic fragment of E. coli AlaRS G237A in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hy1 | ||||||
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Title | Crystal Structure of catalytic fragment of E. coli AlaRS G237A in complex with SerSA | ||||||
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 / Resolution: 2.79 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 | 3hy1.cif.gz | 182.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hy1.ent.gz | 143.9 KB | Display | PDB format |
PDBx/mmJSON format | 3hy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/3hy1 ftp://data.pdbj.org/pub/pdb/validation_reports/hy/3hy1 | HTTPS FTP |
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-Related structure data
Related structure data | 3hxuC 3hxvC 3hxwC 3hxxC 3hxyC 3hxzC 3hy0C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 6 types, 78 molecules
#2: Chemical | ChemComp-SSA / |
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#3: Chemical | ChemComp-HED / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-MES / |
#7: 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: 3.37 Å3/Da / Density % sol: 63.47 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEGMME550, 0.1 M MES, 0.2 M SODIUM SULFATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-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: 2.79→50 Å / Num. obs: 34198 / % possible obs: 99.9 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.097 / Χ2: 1.05 / Net I/σ(I): 29.549 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→46.47 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.218 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.812 / SU B: 13.27 / SU ML: 0.265 / SU R Cruickshank DPI: 0.815 / SU Rfree: 0.351 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.815 / ESU R Free: 0.351 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.97 Å2 / Biso mean: 52.645 Å2 / Biso min: 21.05 Å2
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Refine analyze | Luzzati coordinate error obs: 0.814 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→46.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.79→2.865 Å / Total num. of bins used: 20
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