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- PDB-1e1t: LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH THE LY... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1e1t | ||||||
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Title | LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH THE LYSYL_ADENYLATE INTERMEDIATE | ||||||
![]() | LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE | ||||||
![]() | LIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS | ||||||
Function / homology | ![]() RNA capping / 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 ...RNA capping / 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 / cellular response to heat / nucleic acid binding / tRNA binding / magnesium ion binding / protein homodimerization activity / extracellular space / ATP binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Desogus, G. / Todone, F. / Brick, P. / Onesti, S. | ||||||
![]() | ![]() Title: Active Site of Lysyl-tRNA Synthetase: Structural Studies of the Adenylation Reaction Authors: Desogus, G. / Todone, F. / Brick, P. / Onesti, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.9 KB | Display | ![]() |
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PDB format | ![]() | 91.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 704.5 KB | Display | ![]() |
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Full document | ![]() | 710.1 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e1oSC ![]() 1e22C ![]() 1e24C S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 57767.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A8N6, UniProt: P0A8N5*PLUS, lysine-tRNA ligase |
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-Non-polymers , 5 types, 348 molecules ![](data/chem/img/LAD.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-LAD / | ||||
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#3: Chemical | ChemComp-POP / | ||||
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Details
Compound details | WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING ATP ...WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.8 Å3/Da / Density % sol: 74 % Description: STRUCTURE WAS SOLVED BY DIFFERENCE FOURIER METHODS USING PHASES FROM 1E1O | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.8 Details: THE PROTEIN WAS CONCENTRATED TO 12 MG/ML IN THE PRESENCE OF 5MM LYSINE AND WAS CRYSTALLISED FROM 0.1 M PIPES PH 6.8, 0.5 M LICL, 20% PEG 4K, 17% GLYCEROL; THEN, A SMALL AMOUNT OF A SOLUTION ...Details: THE PROTEIN WAS CONCENTRATED TO 12 MG/ML IN THE PRESENCE OF 5MM LYSINE AND WAS CRYSTALLISED FROM 0.1 M PIPES PH 6.8, 0.5 M LICL, 20% PEG 4K, 17% GLYCEROL; THEN, A SMALL AMOUNT OF A SOLUTION CONTAINING ATP AND MGCL2 WAS ADDED TO THE DROP TO GET A FINAL CONCENTRATION OF ABOUT 5 MM. | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / 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: Jun 15, 1995 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. obs: 41908 / % possible obs: 98.2 % / Redundancy: 8 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.204 / % possible all: 94.1 |
Reflection | *PLUS Num. measured all: 334798 |
Reflection shell | *PLUS % possible obs: 94.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E1O Resolution: 2.4→15 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING ATP AND MG2+, THE ELECTRON DENSITY IN THE ACTIVE SITE CLEARLY SHOWED THAT THE FIRST STEP OF THE ...Details: WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED OVERNIGHT IN A SOLUTION CONTAINING ATP AND MG2+, THE ELECTRON DENSITY IN THE ACTIVE SITE CLEARLY SHOWED THAT THE FIRST STEP OF THE REACTION HAD OCCURRED WITHIN THE CRYSTAL WITH THE FORMATION OF THE LYSYL-ADENYLATE INTERMEDIATE. AN ADDITIONAL ELECTRON DENSITY PEAK COULD BE MODELLED AS A PARTIALLY OCCUPIED PYROPHOSPHATE MOLECULE. THE ASSIGNMENT OF THE ELECTRON DENSITY PEAKS AS MG2+ IONS IS BASED ON THE POSITIONS OBSERVED FOR METAL IONS WHEN THE ELECTRON- DENSE MN2+ IONS WERE USED.
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Refine analyze | Luzzati d res low obs: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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