[English] 日本語
Yorodumi- PDB-7f96: Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f96 | ||||||
---|---|---|---|---|---|---|---|
Title | Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L95 | ||||||
Components | Proline--tRNA ligase | ||||||
Keywords | LIGASE / PROTEIN TRANSLATION / MALARIA / INHIBITOR / PRS | ||||||
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 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.577 Å | ||||||
Authors | Mishra, S. / Malhotra, N. / Manickam, Y. / Sharma, A. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: To Be Published Title: PfPRS with ATP binding pocket inhibitor Authors: Mishra, S. / Malhotra, N. / Manickam, Y. / Sharma, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7f96.cif.gz | 212.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7f96.ent.gz | 171.1 KB | Display | PDB format |
PDBx/mmJSON format | 7f96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/7f96 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/7f96 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ydqS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 57801.188 Da / Num. of mol.: 1 / Fragment: UNP residues 254-746 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: proRS, PFL0670c / Plasmid: PETM41 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I5R7, proline-tRNA ligase |
---|---|
#2: Chemical | ChemComp-JE6 / ~{ |
#3: Chemical | ChemComp-PRO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.1 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Tris (base); BICINE) and 30 % v/v ...Details: 0.2 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Tris (base); BICINE) and 30 % v/v Precipitant Mix (40% v/v Ethylene glycol; 20% w/v PEG 8000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.577→48.542 Å / Num. obs: 25534 / % possible obs: 99.4 % / Redundancy: 19.5 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.084 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2.58→2.64 Å / Redundancy: 17.1 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1720 / CC1/2: 0.93 / Rrim(I) all: 0.844 / % possible all: 92.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YDQ Resolution: 2.577→38.542 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.57 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.82 Å2 / Biso mean: 62.1279 Å2 / Biso min: 29.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.577→38.542 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|