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Yorodumi- PDB-1m83: Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m83 | ||||||
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Title | Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ATP in a Closed, Pre-transition State Conformation | ||||||
Components | Tryptophan-tRNA ligase | ||||||
Keywords | LIGASE / Aminoacyl-tRNA Synthetase / ATP binding site / Rossmann Fold | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SIR / Resolution: 2.2 Å | ||||||
Authors | Retailleau, P. / Huang, X. / Yin, Y. / Hu, M. / Weinreb, V. / Vachette, P. / Vonrhein, C. / Bricogne, G. / Roversi, P. / Ilyin, V. / Carter Jr., C.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations. Authors: Retailleau, P. / Huang, X. / Yin, Y. / Hu, M. / Weinreb, V. / Vachette, P. / Vonrhein, C. / Bricogne, G. / Roversi, P. / Ilyin, V. / Carter, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m83.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m83.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 1m83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m83_validation.pdf.gz | 790.5 KB | Display | wwPDB validaton report |
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Full document | 1m83_full_validation.pdf.gz | 797.6 KB | Display | |
Data in XML | 1m83_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 1m83_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/1m83 ftp://data.pdbj.org/pub/pdb/validation_reports/m8/1m83 | 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: 37225.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: P00953, tryptophan-tRNA ligase | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-ATP / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: microdialysis / pH: 7.5 Details: sodium citrate, sodium atp, magnesium chloride, pH 7.5, MICRODIALYSIS, temperature 310K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 35 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SIR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→45 Å / Num. all: 24329 / Num. obs: 19650 / % possible obs: 80.8 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 32.1 Å2 / Rsym value: 0.08 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 285 / Rsym value: 0.31 / % possible all: 12.1 |
Reflection | *PLUS Lowest resolution: 45 Å / Num. obs: 24329 / % possible obs: 97.5 % / Num. measured all: 303099 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 12.1 % / Rmerge(I) obs: 0.31 |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 2.2→20 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |