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Yorodumi- PDB-4ydq: Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ydq | ||||||
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Title | Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum in complex with Halofuginone and AMPPNP | ||||||
Components | Proline--tRNA ligase | ||||||
Keywords | LIGASE / Prolyl-tRNA synthetase / Complex / Halofuginone / Malaria | ||||||
Function / homology | Function and homology information Ala-tRNA(Pro) hydrolase activity / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Jain, V. / Yogavel, M. / Sharma, A. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Structure of Prolyl-tRNA Synthetase-Halofuginone Complex Provides Basis for Development of Drugs against Malaria and Toxoplasmosis Authors: Jain, V. / Yogavel, M. / Oshima, Y. / Kikuchi, H. / Touquet, B. / Hakimi, M.A. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ydq.cif.gz | 220.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ydq.ent.gz | 171.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ydq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/4ydq ftp://data.pdbj.org/pub/pdb/validation_reports/yd/4ydq | HTTPS FTP |
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-Related structure data
Related structure data | 4twaS 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: 57801.188 Da / Num. of mol.: 2 / Fragment: UNP residues 254-746 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: isolate 3D7 / Gene: proRS, PFL0670c / Plasmid: pETM41 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q8I5R7, proline-tRNA ligase #2: Chemical | #3: Chemical | #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: 2.67 Å3/Da / Density % sol: 53.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5, 2 % (v/v) Tacsimate pH 5.0 and 12 % (w/v) Polyethylene glycol 3,350. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 8, 2014 / Details: Vari Max HR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Vari Max HR mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 54085 / % possible obs: 99.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 35.93 Å2 / Rmerge(I) obs: 0.09 / Χ2: 1.389 / Net I/av σ(I): 21.209 / Net I/σ(I): 10.2 / Num. measured all: 314774 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TWA Resolution: 2.3→27.82 Å / FOM work R set: 0.7991 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.81 Å2 / Biso mean: 44.78 Å2 / Biso min: 18.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→27.82 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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