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- PDB-7wal: Glutamyl-tRNA synthetase from Plasmodium falciparum (PfERS) in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wal | ||||||
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Title | Glutamyl-tRNA synthetase from Plasmodium falciparum (PfERS) in complex with Co | ||||||
![]() | Glutamyl-tRNA synthetase | ||||||
![]() | LIGASE / ERS / GluRS / GLUTAMYL-TRNA SYNTHETASE / AMINOACYL-TRNA SYNTHETAS / AMINOACYLATION / Cobalt | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharma, V. / Manickam, Y. / Babbar, P. / Sharma, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 211.1 KB | Display | ![]() |
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PDB format | ![]() | 166 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7waiC ![]() 7wajC ![]() 7wakC ![]() 7waoC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-CO / #3: Chemical | #4: Chemical | ChemComp-BME / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.77 % |
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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: ![]() ![]() ![]() |
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: 2.29→46.1 Å / Num. obs: 29435 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 1 / Rrim(I) all: 0.07 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.29→2.35 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2036 / CC1/2: 0.69 / Rrim(I) all: 1.378 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: INYL Resolution: 2.29→46.098 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.25 / 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: 174.17 Å2 / Biso mean: 77.0435 Å2 / Biso min: 46.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.29→46.098 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: -27.4565 Å / Origin y: -11.369 Å / Origin z: 20.1246 Å
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Refinement TLS group | Selection details: all |