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Yorodumi- PDB-3knf: Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium fa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3knf | ||||||
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Title | Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium falciparum | ||||||
Components | D-tyrosyl-tRNA(Tyr) deacylase | ||||||
Keywords | HYDROLASE / D-AMINO ACID / DEACYLASE | ||||||
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: 3 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 | 3knf.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3knf.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 3knf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/3knf ftp://data.pdbj.org/pub/pdb/validation_reports/kn/3knf | HTTPS FTP |
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-Related structure data
Related structure data | 3knpC 3ko3C 3ko4C 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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1 |
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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 |
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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: 2.06 Å3/Da / Density % sol: 40.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 3350, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 7, 2008 / Details: Mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 18085 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.108 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.563 / Num. unique all: 1777 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PfDTD-Iodide model (not deposited) Resolution: 3→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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