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Yorodumi- PDB-3a05: Crystal structure of tryptophanyl-tRNA synthetase from hypertherm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a05 | ||||||
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Title | Crystal structure of tryptophanyl-tRNA synthetase from hyperthermophilic archaeon, Aeropyrum pernix K1 complex with tryptophan | ||||||
Components | Tryptophanyl-tRNA synthetase | ||||||
Keywords | LIGASE / TRYPTOPHANYL-TRNA SYNTHETASE / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Nucleotide-binding / Protein biosynthesis | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Tsuchiya, W. / Fujimoto, Z. / Hasegawa, T. | ||||||
Citation | Journal: To be Published Title: Crystal structure of tryptophanyl-tRNA synthetase from hyperthermophilic archaeon, Aeropyrum pernix K1 Authors: Tsuchiya, W. / Fujimoto, Z. / Hasegawa, T. #1: Journal: J.Biochem. / Year: 2009 Title: Molecular Recognition of Tryptophan tRNA by Tryptophanyl-tRNA Synthetase from Aeropyrum pernix K1 Authors: Tsuchiya, W. / Hasegawa, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a05.cif.gz | 93.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a05.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 3a05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a05_validation.pdf.gz | 464.6 KB | Display | wwPDB validaton report |
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Full document | 3a05_full_validation.pdf.gz | 470.2 KB | Display | |
Data in XML | 3a05_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 3a05_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/3a05 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/3a05 | HTTPS FTP |
-Related structure data
Related structure data | 3a04SC 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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Unit cell |
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-Components
#1: Protein | Mass: 42217.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: trpS, APE_2461.1 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y924, tryptophan-tRNA ligase | ||
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#2: Chemical | ChemComp-TRP / | ||
#3: Chemical | ChemComp-SF4 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 100mM Imidazole (pH6.6), 5% PEG6000, 5mM Cadmium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97898 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97898 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 25251 / % possible obs: 98.8 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 44.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 7.6 / Num. unique all: 2309 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3A04 Resolution: 2.2→49.09 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.619 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.107 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→49.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.195→2.252 Å / Total num. of bins used: 20
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