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Open data
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Basic information
Entry | Database: PDB / ID: 1bbw | ||||||
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Title | LYSYL-TRNA SYNTHETASE (LYSS) | ||||||
![]() | PROTEIN (LYSYL-TRNA SYNTHETASE) | ||||||
![]() | LIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS | ||||||
Function / homology | ![]() ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / tRNA aminoacylation for protein translation / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / ligase activity / tRNA binding ...ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / tRNA aminoacylation for protein translation / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / ligase activity / tRNA binding / magnesium ion binding / protein homodimerization activity / extracellular space / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Onesti, S. / Desogus, G. / Brevet, A. / Chen, J. / Plateau, P. / Blanquet, S. / Brick, P. | ||||||
![]() | ![]() Title: Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding. Authors: Onesti, S. / Desogus, G. / Brevet, A. / Chen, J. / Plateau, P. / Blanquet, S. / Brick, P. #1: ![]() Title: Crystal Structure of the Lysyl-tRNA Synthetase (Lysu) from Escherichia Coli Authors: Onesti, S. / Miller, A.D. / Brick, P. #2: ![]() Title: Comparison of the Enzymatic Properties of Two Escherichia Coli Lysyl-tRNA Synthetase Species Authors: Brevet, A. / Chen, J. / Leveque, F. / Blanquet, S. / Plateau, 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 | ![]() | 106.9 KB | Display | ![]() |
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PDB format | ![]() | 81.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.5 KB | Display | ![]() |
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Full document | ![]() | 425.1 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 28.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bbuC ![]() 1lylS C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 57546.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.31 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 68 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRROR |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 25416 / % possible obs: 99.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.7→2.84 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.26 / % possible all: 99.2 |
Reflection | *PLUS Num. measured all: 108202 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.26 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LYL Resolution: 2.7→15 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION APPLIED
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Refine analyze | Luzzati d res low obs: 15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.7 Å / Rfactor Rfree: 0.446 / % reflection Rfree: 5 % / Rfactor Rwork: 0.451 |