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- PDB-8i2m: The crystal structure of homodimeric E. coli tryptophanyl-tRNA sy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i2m | ||||||
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Title | The crystal structure of homodimeric E. coli tryptophanyl-tRNA synthetase bound with niraparib at one of its two active sites | ||||||
![]() | Tryptophan--tRNA ligase | ||||||
![]() | LIGASE / tryptophanyl-tRNA synthetase / fragment screening / antibacterials | ||||||
Function / homology | ![]() tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xiang, M. / Zhou, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening. Authors: Xiang, M. / Xia, K. / Chen, B. / Luo, Z. / Yu, Y. / Jiang, L. / 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 | ![]() | 147.5 KB | Display | ![]() |
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PDB format | ![]() | 111.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8i1wC ![]() 8i1yC ![]() 8i1zC ![]() 8i27C ![]() 8i2aC ![]() 8i2cC ![]() 8i2jC ![]() 8i2lC ![]() 8i4iC ![]() 5v0iS 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
#1: Protein | Mass: 38373.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-3JD / | #3: Chemical | #4: Chemical | ChemComp-TYM / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.27 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 0.16M Ammonium sulfate, 0.1M HEPES pH 7.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 42029 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.994 / Rpim(I) all: 0.052 / Rrim(I) all: 0.121 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.1→2.21 Å / % possible obs: 100 % / Redundancy: 3.2 % / Num. measured all: 19573 / Num. unique obs: 6115 / CC1/2: 0.766 / Rpim(I) all: 0.31 / Rrim(I) all: 0.57 / Net I/σ(I) obs: 2.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5V0I Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.183 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 20.242 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→50 Å
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Refine LS restraints |
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