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Open data
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Basic information
Entry | Database: PDB / ID: 1n3l | ||||||
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Title | Crystal structure of a human aminoacyl-tRNA synthetase cytokine | ||||||
![]() | tyrosyl-tRNA synthetase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, X.-L. / Skene, R.J. / McRee, D.E. / Schimmel, P. | ||||||
![]() | ![]() Title: Crystal structure of a human aminoacyl-tRNA synthetase cytokine Authors: Yang, X.-L. / Skene, R.J. / McRee, D.E. / Schimmel, P. | ||||||
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 | ![]() | 122.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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Components on special symmetry positions |
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Details | The other monomer of the dimer is generated by the two fold axis: -x, -y, z |
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Components
#1: Protein | Mass: 42133.559 Da / Num. of mol.: 1 / Fragment: mini TyrRS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 51.89 % |
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Crystal grow![]() | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.38 Details: (NH4)2SO4, NaH2PO4, K2HPO4, acetone, pH 6.38, VAPOR DIFFUSION, SITTING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 31, 2002 / Details: flat mirror (vertical focusing) |
Radiation | Monochromator: single crystal Si(111) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.18→30 Å / Num. all: 134129 / Num. obs: 134129 / % possible obs: 92.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 55.2 |
Reflection shell | Resolution: 1.18→1.22 Å / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.004 / Num. unique all: 8418 / Rsym value: 0.699 / % possible all: 59 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 93 % |
Reflection shell | *PLUS % possible obs: 59 % / Mean I/σ(I) obs: 1 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Refinement step | Cycle: LAST / Resolution: 1.18→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree![]() ![]() | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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