+Open data
-Basic information
Entry | Database: PDB / ID: 1b70 | ||||||
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Title | PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINE | ||||||
Components | (PHENYLALANYL-TRNA SYNTHETASE) x 2 | ||||||
Keywords | LIGASE / ENZYME / TRNA SYNTHETASE / DIMER OF ALPHA/BETA HETERODIMERS | ||||||
Function / homology | Function and homology information phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Reshetnikova, L. / Moor, N. / Lavrik, O. / Vassylyev, D.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue Authors: Reshetnikova, L. / Moor, N. / Lavrik, O. / Vassylyev, D.G. #1: Journal: Structure / Year: 1997 Title: The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe. Authors: Goldgur, Y. / Mosyak, L. / Reshetnikova, L. / Ankilova, V. / Lavrik, O. / Khodyreva, S. / Safro, M. #2: Journal: Nature New Biol. / Year: 1995 Title: Structure of Phenylalanyl-tRNA Synthetase from Thermus Thermophilus Authors: Mosyak, L. / Reshetnikova, L. / Goldgur, Y. / Delarue, M. / Safro, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b70.cif.gz | 219.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b70.ent.gz | 173.2 KB | Display | PDB format |
PDBx/mmJSON format | 1b70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/1b70 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/1b70 | HTTPS FTP |
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-Related structure data
Related structure data | 1b7yC 1pysS S: Starting model for refinement 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
#1: Protein | Mass: 39309.199 Da / Num. of mol.: 1 / Fragment: ALPHA SUBUNIT / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Cellular location: CYTOPLASM / References: UniProt: P27001, phenylalanine-tRNA ligase |
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#2: Protein | Mass: 86720.656 Da / Num. of mol.: 1 / Fragment: BETA SUBUNIT / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Cellular location: CYTOPLASM / References: UniProt: P27002, phenylalanine-tRNA ligase |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-PHE / |
#5: 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: 3.8 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 313 K / Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALS WERE GROWN BY THE HANGING-DROP TECHNIQUE AT 4O C WITH AMMONIUM SULFATE AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 M L) AT A PROTEIN CONCENTRTION ...Details: CRYSTALS WERE GROWN BY THE HANGING-DROP TECHNIQUE AT 4O C WITH AMMONIUM SULFATE AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 M L) AT A PROTEIN CONCENTRTION OF 3 TO 5 MG PER ML IN 20 AMM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED AMMONIUM SULFATE WAS EQUILIBRATED WITH 1 ML 25 TO 30% SATURATED AMMONIUM SULFATE IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO MAXIMAL DIMENSIONS (0.4MMX0.4MMX0.25 MM) IN A FEW WEEKS., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 75 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 / Details: Chernaya, M., (1987) J. Mol. Biol., 198, 555. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 81613 / % possible obs: 89.4 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.7→2.82 Å / Redundancy: 3 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2.2 / % possible all: 86.2 |
Reflection shell | *PLUS % possible obs: 86.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PYS Resolution: 2.7→50 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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