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Yorodumi- PDB-4rrf: Editing domain of threonyl-tRNA synthetase from Methanococcus jan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rrf | ||||||
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Title | Editing domain of threonyl-tRNA synthetase from Methanococcus jannaschii 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 / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Ahmad, S. / Yerabham, A.S.K. / 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 | 4rrf.cif.gz | 186.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rrf.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rrf_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 4rrf_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 4rrf_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 4rrf_validation.cif.gz | 53 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/4rrf ftp://data.pdbj.org/pub/pdb/validation_reports/rr/4rrf | HTTPS FTP |
-Related structure data
Related structure data | 4rr6C 4rr7C 4rr8C 4rr9C 4rraC 4rrbC 4rrcC 4rrdC 4rrgC 4rrhC 4rriC 4rrjC 4rrkC 4rrlC 4rrmC 4rrqC 4rrrC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 15951.302 Da / Num. of mol.: 6 / Fragment: UNP residues 1-141 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: thrS, MJ1197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58597, threonine-tRNA ligase #2: Chemical | ChemComp-A3S / #3: Chemical | ChemComp-CL / | #4: Chemical | #5: 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: 2.1 Å3/Da / Density % sol: 41.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris HCl, 0.2M MgCl2, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 6, 2011 |
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: 1.7→25 Å / Num. all: 83269 / Num. obs: 75775 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.75 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.136 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→25 Å
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Refine LS restraints |
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