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Yorodumi- PDB-1maw: Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1maw | ||||||
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Title | Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ATP in an Open Conformation | ||||||
Components | TRYPTOPHAN-TRNA LIGASE | ||||||
Keywords | LIGASE / Amino-acyl tRNA synthetase / Rossmann fold / atp 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: 3 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 | 1maw.cif.gz | 380.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1maw.ent.gz | 313.3 KB | Display | PDB format |
PDBx/mmJSON format | 1maw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1maw_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 1maw_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 1maw_validation.xml.gz | 77.6 KB | Display | |
Data in CIF | 1maw_validation.cif.gz | 99.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/1maw ftp://data.pdbj.org/pub/pdb/validation_reports/ma/1maw | HTTPS FTP |
-Related structure data
Related structure data | 1m83C 1mauC 1mb2C 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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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-ATP / |
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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: 54.91 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: microdialysis / pH: 6.6 Details: potassium phosphate, mg-atp, 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: 2.99→15.05 Å / Num. obs: 42607 / % possible obs: 87.1 % / Biso Wilson estimate: 48.3 Å2 / Rsym value: 0.079 |
Reflection | *PLUS Highest resolution: 3 Å / % possible obs: 87.3 % / Num. measured all: 102635 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.11 Å / % possible obs: 70.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D2R Resolution: 3→15 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 41.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 15 Å / Num. reflection obs: 38186 / % reflection Rfree: 10 % / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.154 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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