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Yorodumi- PDB-5xaq: Crystal structure of Animalia-specific tRNA deacylase from Mus mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xaq | ||||||
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Title | Crystal structure of Animalia-specific tRNA deacylase from Mus musculus | ||||||
Components | Probable D-tyrosyl-tRNA(Tyr) deacylase 2 | ||||||
Keywords | HYDROLASE / tRNA / deacylase | ||||||
Function / homology | Function and homology information aminoacyl-tRNA metabolism involved in translational fidelity / Ala-tRNA(Thr) hydrolase activity / D-tyrosyl-tRNA(Tyr) deacylase activity / D-aminoacyl-tRNA deacylase / tRNA metabolic process / aminoacyl-tRNA editing activity / tRNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Kuncha, K.S. / Kattula, B. / Sankarnarayanan, R. | ||||||
Funding support | India, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia Authors: Kuncha, S.K. / Mazeed, M. / Singh, R. / Kattula, B. / Routh, S.B. / Sankaranarayanan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xaq.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xaq.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xaq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xaq_validation.pdf.gz | 434.7 KB | Display | wwPDB validaton report |
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Full document | 5xaq_full_validation.pdf.gz | 436.3 KB | Display | |
Data in XML | 5xaq_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5xaq_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/5xaq ftp://data.pdbj.org/pub/pdb/validation_reports/xa/5xaq | HTTPS FTP |
-Related structure data
Related structure data | 4nbiS S: Starting model for refinement |
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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: 18258.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dtd2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: Q8BHA3, Hydrolases; Acting on ester bonds #2: 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: 2.32 Å3/Da / Density % sol: 46.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: BICINE (pH 8.0), PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→60.94 Å / Num. obs: 29268 / % possible obs: 89.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.4 / % possible all: 51.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NBI Resolution: 1.86→60.94 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.778 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.175 / ESU R Free: 0.162 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.403 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→60.94 Å
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Refine LS restraints |
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