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Yorodumi- PDB-1e24: LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM complexed with lysine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+24 | ||||||
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Title | LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM complexed with lysine and ATP and MN2+ | ||||||
Components | LYSYL-TRNA SYNTHETASE | ||||||
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 / nucleic acid binding / tRNA 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 / nucleic acid binding / tRNA binding / magnesium ion binding / protein homodimerization activity / ATP binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.35 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 | 1e24.cif.gz | 118.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e24.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e24_validation.pdf.gz | 924.2 KB | Display | wwPDB validaton report |
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Full document | 1e24_full_validation.pdf.gz | 928 KB | Display | |
Data in XML | 1e24_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 1e24_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/1e24 ftp://data.pdbj.org/pub/pdb/validation_reports/e2/1e24 | HTTPS FTP |
-Related 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: K12 / Cellular location: CYTOPLASM / Gene: LYSU / Plasmid: PXLYS5 / Gene (production host): LYSU / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG2 References: UniProt: P14825, UniProt: P0A8N5*PLUS, lysine-tRNA ligase |
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-Non-polymers , 5 types, 367 molecules
#2: Chemical | ChemComp-LYS / | ||||
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#3: Chemical | ChemComp-ATP / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Compound details | WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED IN A SOLUTION CONTAINING ATP AND MNCL2 ...WHEN CRYSTALS GROWN IN THE PRESENCE OF LYSINE WERE SOAKED 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 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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 MNCL2 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: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1998 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→65 Å / Num. obs: 45104 / % possible obs: 99.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 7.3 / Rsym value: 0.182 / % possible all: 99 |
Reflection | *PLUS Num. measured all: 217414 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.35→25 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THREE WELL DEFINED ELECTRON DENSITY PEAKS WERE OBSERVED ANDINTERPRETED AS MN2+ IONS. ONE IS COORDINATED BY THE ALPHA AND BETA PHOSPHATE AND TWO CARBOXYLATE (GLU 414 AND GLU 421) AND THE ...Details: THREE WELL DEFINED ELECTRON DENSITY PEAKS WERE OBSERVED ANDINTERPRETED AS MN2+ IONS. ONE IS COORDINATED BY THE ALPHA AND BETA PHOSPHATE AND TWO CARBOXYLATE (GLU 414 AND GLU 421) AND THE OTHER TWO BRIDGE THE BETA AND GAMMA PHOSPHATES.
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Refine analyze | Luzzati d res low obs: 25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.46 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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