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Yorodumi- PDB-4rrq: K121M mutant of N-terminal editing domain of threonyl-tRNA synthe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rrq | ||||||
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Title | K121M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi with L-Ser3AA | ||||||
Components | Threonine--tRNA ligase | ||||||
Keywords | LIGASE / DTD-like fold / Proofreading | ||||||
Function / homology | Function and homology information threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi GE5 (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Hussain, T. / Kamarthapu, V. / Sankaranarayanan, R. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme. Authors: Ahmad, S. / Muthukumar, S. / Kuncha, S.K. / Routh, S.B. / Yerabham, A.S. / Hussain, T. / Kamarthapu, V. / Kruparani, S.P. / Sankaranarayanan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rrq.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rrq.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rrq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rrq_validation.pdf.gz | 997.5 KB | Display | wwPDB validaton report |
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Full document | 4rrq_full_validation.pdf.gz | 998.8 KB | Display | |
Data in XML | 4rrq_validation.xml.gz | 16 KB | Display | |
Data in CIF | 4rrq_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/4rrq ftp://data.pdbj.org/pub/pdb/validation_reports/rr/4rrq | HTTPS FTP |
-Related structure data
Related structure data | 4rr6C 4rr7C 4rr8C 4rr9C 4rraC 4rrbC 4rrcC 4rrdC 4rrfC 4rrgC 4rrhC 4rriC 4rrjC 4rrkC 4rrlC 4rrmC 4rrrC 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: 16740.328 Da / Num. of mol.: 2 / Fragment: UNP residues 1-147 / Mutation: K121M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / Gene: thrS, PYRAB13430, PAB1490 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UZ14, threonine-tRNA ligase #2: Chemical | #3: 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: 2.18 Å3/Da / Density % sol: 43.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: BisTris, NaCl, PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2009 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→25 Å / Num. all: 28360 / Num. obs: 27566 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→25 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.79→25 Å
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