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Yorodumi- PDB-1e1t: LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH THE LY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e1t | ||||||
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Title | LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH THE LYSYL_ADENYLATE INTERMEDIATE | ||||||
Components | LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE | ||||||
Keywords | LIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS | ||||||
Function / homology | Function and homology information RNA capping / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ligase activity / cellular response to heat / tRNA binding / nucleic acid binding / magnesium ion binding ...RNA capping / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ligase activity / cellular response to heat / tRNA binding / nucleic acid binding / magnesium ion binding / protein homodimerization activity / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Desogus, G. / Todone, F. / Brick, P. / Onesti, S. | ||||||
Citation | Journal: Biochemistry / Year: 2000 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e1t.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e1t.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/1e1t ftp://data.pdbj.org/pub/pdb/validation_reports/e1/1e1t | HTTPS FTP |
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-Related structure data
Related structure data | 1e1oSC 1e22C 1e24C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Cellular location: CYTOPLASM / Gene: LYSU / Plasmid: PXLYS5 / Gene (production host): LYSU / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG2 References: UniProt: P0A8N6, UniProt: P0A8N5*PLUS, lysine-tRNA ligase |
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-Non-polymers , 5 types, 348 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.93 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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