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- PDB-4twa: Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4twa | ||||||
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Title | Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum | ||||||
![]() | Proline--tRNA ligase | ||||||
![]() | LIGASE / Protein translation / Halofuginone / Malaria / Inhibitor / PRS / Synthetase | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jain, V. / Yogavel, M. / Sharma, A. | ||||||
![]() | ![]() Title: Structural and functional analysis of the anti-malarial drug target prolyl-tRNA synthetase. Authors: Jain, V. / Kikuchi, H. / Oshima, Y. / Sharma, A. / Yogavel, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 399.6 KB | Display | ![]() |
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PDB format | ![]() | 326.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4k86S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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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.) ![]() ![]() Strain: isolate 3D7 / Gene: proRS, PFL0670c / Plasmid: pETM41 / Production host: ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.8 M lithium sulphate monohydrate and 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 30738 / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 4K86 Resolution: 3→38.79 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→38.79 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 35.2759 Å / Origin y: 22.1673 Å / Origin z: 32.9794 Å
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Refinement TLS group | Selection details: all |