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- PDB-7wpt: Methionyl-tRNA synthetase from Staphylococcus aureus complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wpt | |||||||||
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Title | Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a fragment M2-80 and ATP | |||||||||
![]() | Methionine--tRNA ligase | |||||||||
![]() | LIGASE/INHIBITOR / LIGASE-INHIBITOR COMPLEX | |||||||||
Function / homology | ![]() methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yi, J. / Cai, Z. / Qiu, H. / Lu, F. / Chen, B. / Luo, Z. / Gu, Q. / Xu, J. / Zhou, H. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.9 KB | Display | ![]() |
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PDB format | ![]() | 85.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 997.4 KB | Display | ![]() |
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Full document | ![]() | 1016.6 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wpiC ![]() 7wpjC ![]() 7wpkC ![]() 7wplC ![]() 7wpmSC ![]() 7wpnC ![]() 7wpxC ![]() 7wq0C S: Starting model for refinement 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
-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.) ![]() Strain: COL / Gene: metG / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 42 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/XM0.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/XM0.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ATP / | ||||
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#3: Chemical | ChemComp-XM0 / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.72 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→64.31 Å / Num. obs: 24773 / % possible obs: 93.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.26→2.409 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3 / Num. unique obs: 4141 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7WPM Resolution: 2.26→64.31 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.077 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.383 / ESU R Free: 0.261 / 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: 101.98 Å2 / Biso mean: 45.547 Å2 / Biso min: 28.16 Å2
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Refinement step | Cycle: final / Resolution: 2.26→64.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.263→2.322 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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