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Yorodumi- PDB-2yy5: Crystal Structure of tryptophanyl-tRNA synthetase from Mycoplasma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yy5 | ||||||
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Title | Crystal Structure of tryptophanyl-tRNA synthetase from Mycoplasma pneumoniae | ||||||
Components | Tryptophanyl-tRNA synthetase | ||||||
Keywords | LIGASE / Aminoaccyl tRNA synthetase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Ishii, T. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of tryptophanyl-tRNA synthetase from Mycoplasma pneumoniae Authors: Ishii, T. / Bessho, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yy5.cif.gz | 290.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yy5.ent.gz | 235.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/2yy5 ftp://data.pdbj.org/pub/pdb/validation_reports/yy/2yy5 | HTTPS FTP |
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-Related structure data
Related structure data | 1i6mS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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: 39311.434 Da / Num. of mol.: 4 / Mutation: P240S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) Strain: M129 / Plasmid: pUC18 / Production host: cell free system (unknown) / References: UniProt: P75510, tryptophan-tRNA ligase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-WSA / #4: 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: 2.82 Å3/Da / Density % sol: 56.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 0.15M Ammonium Sulfate, 18% PEG3350, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2006 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 58085 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 18.3 Å2 / Rsym value: 0.103 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 3.2 % / Num. unique all: 5771 / Rsym value: 0.258 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I6M Resolution: 2.55→34.03 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 33096 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.0512 Å2 / ksol: 0.333735 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→34.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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