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Yorodumi- PDB-7wpn: Methionyl-tRNA synthetase from Staphylococcus aureus complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wpn | |||||||||
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Title | Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a phenylbenzimidazole inhibitor and ATP | |||||||||
Components | Methionine--tRNA ligase | |||||||||
Keywords | LIGASE/INHIBITOR / LIGASE-INHIBITOR COMPLEX | |||||||||
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 subsp. aureus COL (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 7wpn.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wpn.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 7wpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/7wpn ftp://data.pdbj.org/pub/pdb/validation_reports/wp/7wpn | HTTPS FTP |
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-Related structure data
Related structure data | 7wpiC 7wpjC 7wpkC 7wplC 7wpmSC 7wptC 7wpxC 7wq0C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61103.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria) Strain: COL / Gene: metG / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HII6, methionine-tRNA ligase |
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-Non-polymers , 5 types, 32 molecules
#2: Chemical | ChemComp-ATP / |
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#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-29I / ( |
#5: Chemical | ChemComp-ACY / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.27 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium cacodylate, PEG 3350 |
-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: May 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→61.13 Å / Num. obs: 20367 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2082 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WPM Resolution: 2.4→61.13 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.879 / SU B: 9.511 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.574 / ESU R Free: 0.288 / 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: 63.24 Å2 / Biso mean: 21.865 Å2 / Biso min: 7.94 Å2
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Refinement step | Cycle: final / Resolution: 2.4→61.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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