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Yorodumi- PDB-1yi8: Crystal structure of tryptophanyl trRNA synthetase II from Deinoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yi8 | ||||||
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Title | Crystal structure of tryptophanyl trRNA synthetase II from Deinococcus radiodurans in complex with L-Trp | ||||||
Components | tryptophanyl-tRNA synthetase | ||||||
Keywords | LIGASE / Auxiliary tryptophanyl trna synthetase | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Buddha, M.R. / Crane, B.R. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2005 Title: Structure and activity of an aminoacyl-tRNA synthetase that charges tRNA with nitro-tryptophan. Authors: Buddha, M.R. / Crane, B.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yi8.cif.gz | 220.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yi8.ent.gz | 176.6 KB | Display | PDB format |
PDBx/mmJSON format | 1yi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/1yi8 ftp://data.pdbj.org/pub/pdb/validation_reports/yi/1yi8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38225.586 Da / Num. of mol.: 3 / Fragment: Enzyme Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: R1 / Gene: DR1093 / Plasmid: pet28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RVD6 #2: Chemical | ChemComp-TRP / | #3: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 20% PEG4K, 0.2M DiAMMONIUM HYDROGEN PHOSPHATE, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 12, 2004 | ||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. all: 90200 / Num. obs: 72160 / % possible obs: 80 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.056 / Net I/σ(I): 20.4 | ||||||||||||||||||
Reflection shell | Resolution: 2.1→2.5 Å / Redundancy: 2 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.21 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å
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