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Yorodumi- PDB-7wao: Glutamyl-tRNA synthetase from Plasmodium falciparum (PfERS) in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wao | ||||||
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Title | Glutamyl-tRNA synthetase from Plasmodium falciparum (PfERS) in complex with Mn | ||||||
Components | Glutamyl-tRNA synthetase | ||||||
Keywords | LIGASE / ERS / GluRS / GLUTAMYL-TRNA SYNTHETASE / AMINOACYL-TRNA SYNTHETAS / AMINOACYLATION / Manganese | ||||||
Function / homology | Function and homology information methionyl glutamyl tRNA synthetase complex / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.582 Å | ||||||
Authors | Sharma, V. / Manickam, Y. / Babbar, P. / 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 | 7wao.cif.gz | 216.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wao.ent.gz | 170 KB | Display | PDB format |
PDBx/mmJSON format | 7wao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wao_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 7wao_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 7wao_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 7wao_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/7wao ftp://data.pdbj.org/pub/pdb/validation_reports/wa/7wao | HTTPS FTP |
-Related structure data
Related structure data | 7waiC 7wajC 7wakC 7walC 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: 61361.293 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 (E. coli) / References: UniProt: Q8IDK7, glutamate-tRNA ligase | ||||||
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#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-CL / #4: 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: 2.68 Å3/Da / Density % sol: 54.08 % |
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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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.984 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→45.33 Å / Num. obs: 20654 / % possible obs: 99.2 % / Redundancy: 6.8 % / CC1/2: 1 / Rrim(I) all: 0.123 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.58→2.65 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1370 / CC1/2: 0.69 / Rrim(I) all: 1.224 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NYL Resolution: 2.582→45.329 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.91 / 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: 156.1 Å2 / Biso mean: 72.6913 Å2 / Biso min: 28.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.582→45.329 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: -26.0765 Å / Origin y: -10.1249 Å / Origin z: 19.5027 Å
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Refinement TLS group | Selection details: all |