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Yorodumi- PDB-3hxy: Crystal Structure of catalytic fragment of E. coli AlaRS in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hxy | ||||||
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Title | Crystal Structure of catalytic fragment of E. coli AlaRS in complex with AMPPCP, Ala-AMP and PCP | ||||||
Components | Alanyl-tRNA synthetase | ||||||
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 / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 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 | 3hxy.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hxy.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hxy_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3hxy_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3hxy_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 3hxy_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/3hxy ftp://data.pdbj.org/pub/pdb/validation_reports/hx/3hxy | HTTPS FTP |
-Related structure data
Related structure data | 3hxuC 3hxvC 3hxwC 3hxxC 3hxzC 3hy0C 3hy1C 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49924.055 Da / Num. of mol.: 1 / Fragment: N-terminal Catalytic fragment residues 2-442 / Mutation: H104L, Q108L, E112L 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 , 7 types, 404 molecules
#2: Chemical | ChemComp-5AL / | ||||||
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#3: Chemical | ChemComp-MDN / | ||||||
#4: Chemical | ChemComp-ACP / | ||||||
#5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-HED / | #7: Chemical | ChemComp-BME / | #8: 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: 2.87 Å3/Da / Density % sol: 57.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG 3350, 0.1 M Tris-HCl, 0.2 M Potassium Nitrate, pH 8.5, vapor diffusion, sitting drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 24, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.27→50 Å / Num. obs: 27449 / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 65.368 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.27→41.56 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.205 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS LIGANDS 5AL, MDN, ACP OCCUPY THE SAME SITE
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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 mean: 22.077 Å2
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Refine analyze | Luzzati coordinate error obs: 0.263 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→41.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.329 Å / Total num. of bins used: 20
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