+Open data
-Basic information
Entry | Database: PDB / ID: 7wai | ||||||
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Title | Glutamyl-tRNA synthetase from Plasmodium falciparum (PfERS) | ||||||
Components | Glutamyl-tRNA synthetase | ||||||
Keywords | LIGASE / ERS / GluRS / GLUTAMYL-TRNA SYNTHETASE / AMINOACYL-TRNA SYNTHETAS / AMINOACYLATION | ||||||
Function / homology | Function and homology information methionyl glutamyl tRNA synthetase complex / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å | ||||||
Authors | Sharma, V. / Manickam, Y. / Harlos, K. / Sharma, A. | ||||||
Funding support | India, 1items
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Citation | Journal: Mol.Biochem.Parasitol. / Year: 2022 Title: Structural characterization of glutamyl-tRNA synthetase (GluRS) from Plasmodium falciparum. Authors: Sharma, V.K. / Chhibber-Goel, J. / Yogavel, M. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wai.cif.gz | 225.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wai.ent.gz | 178.7 KB | Display | PDB format |
PDBx/mmJSON format | 7wai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/7wai ftp://data.pdbj.org/pub/pdb/validation_reports/wa/7wai | HTTPS FTP |
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-Related structure data
Related structure data | 7wajC 7wakC 7walC 7waoC 1nylS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 61329.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1349200 / Plasmid: pETM41 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8IDK7, glutamate-tRNA ligase | ||||
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#2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 30 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.105→74.4 Å / Num. obs: 35766 / % possible obs: 92.6 % / Redundancy: 6.3 % / CC1/2: 1 / Rrim(I) all: 0.059 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.105→2.142 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1100 / CC1/2: 0.42 / Rrim(I) all: 2.02 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NYL Resolution: 2.105→45.373 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.55 / 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: 158.76 Å2 / Biso mean: 68.9563 Å2 / Biso min: 38.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.105→45.373 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -26.3118 Å / Origin y: -9.4903 Å / Origin z: 19.9167 Å
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Refinement TLS group | Selection details: all |