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- PDB-1nj2: Crystal structure of Prolyl-tRNA Synthetase from Methanothermobac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nj2 | ||||||
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Title | Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus | ||||||
![]() | Proline-tRNA Synthetase | ||||||
![]() | LIGASE / Class-II tRNA synthetase | ||||||
Function / homology | ![]() proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kamtekar, S. / Kennedy, W.D. / Wang, J. / Stathopoulos, C. / Soll, D. / Steitz, T.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.9 KB | Display | ![]() |
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PDB format | ![]() | 80.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432 KB | Display | ![]() |
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Full document | ![]() | 443.2 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 constructed by a twofold rotation. |
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Components
#1: Protein | Mass: 58170.258 Da / Num. of mol.: 1 / Fragment: N terminally His Tagged Enzyme Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Delta H Description: Strain supplemented with additional plasmid encoding rare tRNAs Gene: MTH611 / Plasmid: pET15b / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.98 Å3/Da / Density % sol: 75.13 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Tris, Beta-Mercaptoethanol, MgCl2,NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12-25 ℃ / pH: 8.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2000 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.945 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. all: 36062 / Num. obs: 35918 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 3.1→3.21 Å / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 3.1 Å |
Reflection shell | *PLUS % possible obs: 99.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Methanocaldococcus janaschii Proline tRNA Synthetase Resolution: 3.11→29.95 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.3074 Å2 / ksol: 0.264032 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.4 Å2
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Refine analyze | Luzzati coordinate error free: 0.52 Å / Luzzati sigma a free: 0.75 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.11→29.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.11→3.29 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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