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Yorodumi- PDB-1mb2: Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mb2 | ||||||
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Title | Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open Conformation | ||||||
Components | TRYPTOPHAN-TRNA LIGASE | ||||||
Keywords | LIGASE / Aminoacyl-tRNA Synthetase / Rossmann fold / amino acid binding site | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 1mb2.cif.gz | 374.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mb2.ent.gz | 310.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mb2_validation.pdf.gz | 501.3 KB | Display | wwPDB validaton report |
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Full document | 1mb2_full_validation.pdf.gz | 570.3 KB | Display | |
Data in XML | 1mb2_validation.xml.gz | 74.4 KB | Display | |
Data in CIF | 1mb2_validation.cif.gz | 96.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/1mb2 ftp://data.pdbj.org/pub/pdb/validation_reports/mb/1mb2 | HTTPS FTP |
-Related structure data
Related structure data | 1m83C 1mauC 1mawC 1d2rS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 37225.672 Da / Num. of mol.: 6 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 #2: Chemical | ChemComp-TRP / |
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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: 2.73 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: microdialysis / pH: 6.6 Details: potassium phosphate, l-tryptophan, pH 6.6, MICRODIALYSIS, temperature 310K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 42 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.585→15.024 Å / Num. obs: 55705 / % possible obs: 83.1 % / Rsym value: 0.071 |
Reflection shell | Resolution: 2.7→2.8 Å / % possible all: 50.4 |
Reflection | *PLUS Highest resolution: 2.7 Å / Num. measured all: 120955 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS % possible obs: 50.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D2R Resolution: 2.7→14.98 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 49.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→14.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 15 Å / Num. reflection obs: 49817 / % reflection Rfree: 10 % / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.173 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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