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Yorodumi- PDB-1nj8: Crystal Structure of Prolyl-tRNA Synthetase from Methanocaldococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nj8 | ||||||
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Title | Crystal Structure of Prolyl-tRNA Synthetase from Methanocaldococcus janaschii | ||||||
Components | Proline-tRNA Synthetase | ||||||
Keywords | LIGASE / Class-II tRNA synthetase | ||||||
Function / homology | Function and homology information proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Kamtekar, S. / Kennedy, W.D. / Wang, J. / Stathopoulos, C. / Soll, D. / Steitz, T.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases Authors: Kamtekar, S. / Kennedy, W.D. / Wang, J. / Stathopoulos, C. / Soll, D. / Steitz, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nj8.cif.gz | 374.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nj8.ent.gz | 307.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/1nj8 ftp://data.pdbj.org/pub/pdb/validation_reports/nj/1nj8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | The biological unit is a dimer. Each asymmetric unit contains two such dimers. |
-Components
#1: Protein | Mass: 53778.809 Da / Num. of mol.: 4 Fragment: N terminally His tagged and Thrombin digested enzyme Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Description: Strain supplemented with additional plasmid encoding rare tRNAs Gene: MJ1238 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 RecA- / References: UniProt: Q58635, proline-tRNA ligase #2: 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: 4.46 Å3/Da / Density % sol: 49.6 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Sodium Acetate, Ammonium Sulfate, PEG 4000, beta-Mercaptoethanol, Tris, Sodium Chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12-25 ℃ / pH: 8.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3.2→20 Å / Num. all: 34834 / Num. obs: 30271 / % possible obs: 86.9 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.9 | ||||||||||||||||||
Reflection shell | Resolution: 3.2→3.31 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / % possible all: 80.3 | ||||||||||||||||||
Reflection | *PLUS Highest resolution: 3.2 Å | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 80.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Thermus Thermophilus Proline tRNA Synthetase Resolution: 3.2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 225015.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: BULK SOLVENT MODELING / Bsol: 10 Å2 / ksol: 0.1854 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 3.2 Å / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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