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Yorodumi- PDB-1jzq: Isoleucyl-tRNA synthetase Complexed with Isoleucyl-adenylate analogue -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jzq | ||||||
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Title | Isoleucyl-tRNA synthetase Complexed with Isoleucyl-adenylate analogue | ||||||
Components | Isoleucyl-tRNA synthetase | ||||||
Keywords | LIGASE / aminoacyl-tRNA synthetase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Nakama, T. / Nureki, O. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase. Authors: Nakama, T. / Nureki, O. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jzq.cif.gz | 178.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jzq.ent.gz | 140.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jzq_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 1jzq_full_validation.pdf.gz | 499.1 KB | Display | |
Data in XML | 1jzq_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 1jzq_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/1jzq ftp://data.pdbj.org/pub/pdb/validation_reports/jz/1jzq | 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
#1: Protein | Mass: 94682.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P56690, isoleucine-tRNA ligase | ||
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#2: Chemical | #3: Chemical | ChemComp-ILA / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 70.03 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2-propanol, PEG4000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: Nureki, O., (1998) Science, 280, 578. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 27250 / % possible obs: 88.3 % |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 40 Å / Num. measured all: 63934 / Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS Rmerge(I) obs: 0.357 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 30 Å / Rfactor obs: 0.22 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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