+Open data
-Basic information
Entry | Database: PDB / ID: 7wpj | |||||||||
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Title | Methionyl-tRNA synthetase from Staphylococcus aureus | |||||||||
Components | Methionine--tRNA ligase | |||||||||
Keywords | LIGASE / Inhibitor | |||||||||
Function / homology | Function and homology information methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Yi, J. / Cai, Z. / Qiu, H. / Lu, F. / Chen, B. / Luo, Z. / Gu, Q. / Xu, J. / Zhou, H. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase. Authors: Yi, J. / Cai, Z. / Qiu, H. / Lu, F. / Luo, Z. / Chen, B. / Gu, Q. / Xu, J. / Zhou, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wpj.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wpj.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 7wpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/7wpj ftp://data.pdbj.org/pub/pdb/validation_reports/wp/7wpj | HTTPS FTP |
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-Related structure data
Related structure data | 7wpiC 7wpkC 7wplC 7wpmC 7wpnC 7wptC 7wpxC 7wq0C 4qreS 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: 61103.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: metG / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HII6, methionine-tRNA ligase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.85 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: sodium cacodylate, PEG 3350 / PH range: 6.2-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→59.73 Å / Num. obs: 14046 / % possible obs: 96 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.65→2.74 Å / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 8.7 / Num. unique obs: 1402 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QRE Resolution: 2.65→59.48 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.846 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.18 Å2 / Biso mean: 21.23 Å2 / Biso min: 5.3 Å2
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Refinement step | Cycle: final / Resolution: 2.65→59.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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