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Yorodumi- PDB-1fyf: CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fyf | ||||||
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Title | CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE COMPLEXED WITH A SERYL ADENYLATE ANALOG | ||||||
Components | THREONYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / AMINO ACID RECOGNITION / ZINC ION / TRNA-SYNTHETASE / ADENYLATE ANALOG / DELETION MUTANT | ||||||
Function / homology | Function and homology information tRNA aminoacylation / aminoacyl-tRNA ligase activity / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding ...tRNA aminoacylation / aminoacyl-tRNA ligase activity / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding / regulation of translation / tRNA binding / response to antibiotic / protein homodimerization activity / RNA binding / zinc ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å | ||||||
Authors | Sankaranarayanan, R. / Dock-Bregeon, A.C. / Moras, D. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2000 Title: Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem. Authors: Dock-Bregeon, A. / Sankaranarayanan, R. / Romby, P. / Caillet, J. / Springer, M. / Rees, B. / Francklyn, C.S. / Ehresmann, C. / Moras, D. #1: Journal: Cell(Cambridge,Mass.) / Year: 1999 Title: The Structure of Threonyl-tRNA Synthetase-tRNA(Thr) Complex Enlightens its Repressor Activity and Reveals an Essential Zinc Ion in the Active Site Authors: Sankaranarayanan, R. / Dock-Bregeon, A.C. / Romby, P. / Caillet, J. / Springer, M. / Rees, B. / Ehresmann, C. / Ehresmann, B. / Moras, D. #2: Journal: Nat.Struct.Biol. / Year: 2000 Title: Zinc Ion Mediated Amino Acid Discrimination by Threonyl-tRNA Synthetase Authors: Sankaranarayanan, R. / Dock-Bregeon, A.C. / Rees, B. / Bovee, M. / Caillet, J. / Romby, P. / Francklyn, C.S. / Moras, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fyf.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fyf.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fyf_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1fyf_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1fyf_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 1fyf_validation.cif.gz | 53.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fyf ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fyf | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | The biological assembly is a dimer which is in the asymmetric unit. |
-Components
#1: Protein | Mass: 46725.180 Da / Num. of mol.: 2 Fragment: CATALYTIC AND ANTICODON BINDING DOMAINS (RESIDUES 242-642) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8M3, threonine-tRNA ligase #2: Chemical | #3: Chemical | #4: 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: 2.94 Å3/Da / Density % sol: 58.14 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: PEG 4000, ammonium acetate, magnesium chloride, pH 6.5, VAPOR DIFFUSION, temperature 277.0K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8439 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 18, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8439 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 127385 / Num. obs: 127385 / % possible obs: 95.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.276 / Num. unique all: 7268 / % possible all: 82.9 |
Reflection | *PLUS Num. measured all: 431526 |
Reflection shell | *PLUS % possible obs: 82.9 % |
-Processing
Software |
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Refinement | Resolution: 1.65→19.93 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2345367.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.55 Å2 / ksol: 0.381 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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