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- PDB-1n9w: Crystal structure of the non-discriminating and archaeal-type asp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n9w | ||||||
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Title | Crystal structure of the non-discriminating and archaeal-type aspartyl-tRNA synthetase from Thermus thermophilus | ||||||
![]() | aspartyl-tRNA synthetase 2 | ||||||
![]() | BIOSYNTHETIC PROTEIN | ||||||
Function / homology | ![]() aspartate-tRNAAsn ligase / aspartate-tRNA(Asn) ligase activity / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / nucleic acid binding / RNA binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Charron, C. / Roy, H. / Blaise, M. / Giege, R. / Kern, D. | ||||||
![]() | ![]() Title: Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain Authors: Charron, C. / Roy, H. / Blaise, M. / Giege, R. / Kern, D. #1: ![]() Title: Crystallization and preliminary X-ray diffraction data of the second and archaebacterial-type aspartyl-tRNA synthetase from Thermus thermophilus Authors: Charron, C. / Roy, H. / Lorber, L. / Kern, D. / Giege, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.9 KB | Display | ![]() |
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PDB format | ![]() | 122.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.2 KB | Display | ![]() |
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Full document | ![]() | 456.5 KB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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 in the asymmetric unit |
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Components
#1: Protein | Mass: 48397.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.45 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: PEG 8000 and NaCl, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: Oct 10, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 53223 / Num. obs: 52274 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.045 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.221 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.221 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å
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Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 45048 / % reflection Rfree: 7 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.2 | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.3 Å |