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Yorodumi- PDB-8i1z: E. coli tryptophanyl-tRNA synthetase bound with a chemical fragment -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i1z | ||||||
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Title | E. coli tryptophanyl-tRNA synthetase bound with a chemical fragment | ||||||
Components | Tryptophan--tRNA ligase | ||||||
Keywords | LIGASE / tryptophanyl-tRNA synthetase / dimer interface / fragment screening / antibacterials | ||||||
Function / homology | Function and homology information tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Xiang, M. / Zhou, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i1z.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i1z.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 8i1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/8i1z ftp://data.pdbj.org/pub/pdb/validation_reports/i1/8i1z | HTTPS FTP |
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-Related structure data
Related structure data | 8i1wC 8i1yC 8i27C 8i2aC 8i2cC 8i2jC 8i2lC 8i2mC 8i4iC 5v0iS 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: 38373.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: trpS, b3384, JW3347 / Production host: Escherichia coli (E. coli) / References: UniProt: P00954, tryptophan-tRNA ligase #2: Chemical | ChemComp-O7R / | #3: Chemical | #4: Chemical | ChemComp-TYM / | #5: Water | ChemComp-HOH / | 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: 2.44 Å3/Da / Density % sol: 49.67 % |
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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: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50.01 Å / Num. obs: 67909 / % possible obs: 99.2 % / Redundancy: 3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.035 / Rrim(I) all: 0.064 / Χ2: 0.89 / Net I/σ(I): 11.6 / Num. measured all: 204490 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible obs: 98.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.374 / Num. measured all: 9006 / Num. unique obs: 4029 / CC1/2: 0.88 / Rpim(I) all: 0.306 / Rrim(I) all: 0.485 / Χ2: 0.78 / Net I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5V0I Resolution: 1.8→50.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.397 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.123 / 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: 34.245 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→50.01 Å
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Refine LS restraints |
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