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Yorodumi- PDB-3ko4: Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium fa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ko4 | ||||||
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Title | Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium falciparum in complex with ADP | ||||||
Components | D-tyrosyl-tRNA(Tyr) deacylase | ||||||
Keywords | HYDROLASE / DTD / Deacylase / ADP | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Manickam, Y. / Bhatt, T.K. / Sharma, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Ligand-bound Structures Provide Atomic Snapshots for the Catalytic Mechanism of D-Amino Acid Deacylase Authors: Bhatt, T.K. / Yogavel, M. / Wydau, S. / Berwal, R. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ko4.cif.gz | 190.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ko4.ent.gz | 153.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ko4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/3ko4 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/3ko4 | HTTPS FTP |
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-Related structure data
Related structure data | 3knfC 3knpC 3ko3C 3ko5C 3ko7C 3ko9C 3kobC 3kocC 3kodC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 19233.084 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: dtd / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: Q8IIS0, Hydrolases; Acting on ester bonds #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: 1.97 Å3/Da / Density % sol: 37.65 % / Mosaicity: 0.943 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25% PEG 3350. 0.1 MES , pH 6.2-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: 6.2-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. obs: 19638 / % possible obs: 81.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.08 / Χ2: 0.876 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.387 / Num. unique all: 1080 / Χ2: 0.729 / % possible all: 44.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PfDTD-iodide model (not deposited) Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.874 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 19.624 / SU ML: 0.408 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.536 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.17 Å2 / Biso mean: 57.401 Å2 / Biso min: 29.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
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