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Yorodumi- PDB-5j61: D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j61 | ||||||
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Title | D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with glycyl-3'-aminoadenosine at 2.10 Angstrom resolution | ||||||
Components | D-tyrosyl-tRNA(Tyr) deacylase | ||||||
Keywords | HYDROLASE / DTD / proofreading / chiral / enantioselection | ||||||
Function / homology | Function and homology information Gly-tRNA(Ala) hydrolase activity / D-tyrosyl-tRNA(Tyr) deacylase activity / D-aminoacyl-tRNA deacylase / tRNA metabolic process / tRNA binding / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Routh, S.B. / Ahmad, S. / Sankaranarayanan, R. | ||||||
Funding support | India, 1items
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Citation | Journal: Plos Biol. / Year: 2016 Title: Elongation Factor Tu Prevents Misediting of Gly-tRNA(Gly) Caused by the Design Behind the Chiral Proofreading Site of D-Aminoacyl-tRNA Deacylase Authors: Routh, S.B. / Pawar, K.I. / Ahmad, S. / Singh, S. / Suma, K. / Kumar, M. / Kuncha, S.K. / Yadav, K. / 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 | 5j61.cif.gz | 262.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j61.ent.gz | 213.6 KB | Display | PDB format |
PDBx/mmJSON format | 5j61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j61_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 5j61_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 5j61_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 5j61_validation.cif.gz | 61.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/5j61 ftp://data.pdbj.org/pub/pdb/validation_reports/j6/5j61 | HTTPS FTP |
-Related structure data
Related structure data | 3knfS S: Starting model for refinement |
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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: 19233.084 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: PF11_0095 / Plasmid: PET-21B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8IIS0, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-A3G / #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: 2.2 Å3/Da / Density % sol: 44.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 28% PEG 3350, 0.4M sodium chloride, 0.1M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 93 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 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. obs: 75606 / % possible obs: 96.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.876 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KNF Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.627 / SU ML: 0.237 / Cross valid method: FREE R-VALUE / ESU R: 0.281 / ESU R Free: 0.223
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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: 59.333 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→25 Å
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Refine LS restraints |
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