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Yorodumi- PDB-1evl: CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1evl | ||||||
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Title | CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE WITH A THREONYL 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å | ||||||
Authors | Sankaranarayanan, R. / Dock-Bregeon, A.C. / Rees, B. / Moras, D. | ||||||
Citation | 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. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1evl.cif.gz | 366.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1evl.ent.gz | 293.5 KB | Display | PDB format |
PDBx/mmJSON format | 1evl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1evl_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1evl_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1evl_validation.xml.gz | 76.1 KB | Display | |
Data in CIF | 1evl_validation.cif.gz | 110.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/1evl ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1evl | HTTPS FTP |
-Related 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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Details | The biological assembly is a dimer and there are two dimers in the asymmetric unit. |
-Components
#1: Protein | Mass: 46725.180 Da / Num. of mol.: 4 Fragment: CATALYTIC AND ANTICODON BINDING DOMAINS (RESIDUES 242-642) Source method: isolated from a genetically manipulated source Details: TRUNCATED FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8M3, threonine-tRNA ligase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-TSB / #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: 3.48 Å3/Da / Density % sol: 64.62 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 4000, Ammonium acetate, magnesium chloride , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
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: 1.55→30 Å / Num. all: 369786 / Num. obs: 366098 / % possible obs: 99 % / Redundancy: 3.31 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 2.04 % / Rmerge(I) obs: 0.218 / Num. unique all: 21980 / % possible all: 89.1 |
Reflection | *PLUS Num. measured all: 1246068 |
Reflection shell | *PLUS % possible obs: 89.1 % |
-Processing
Software |
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Refinement | Resolution: 1.55→30 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2523048 / 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: 46.56 Å2 / ksol: 0.363 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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