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Yorodumi- PDB-7bzj: The Discovery of Benzhydrol-Oxaborole Hybrid Derivatives as Leucy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bzj | |||||||||
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Title | The Discovery of Benzhydrol-Oxaborole Hybrid Derivatives as Leucyl-tRNA Synthetase Inhibitors | |||||||||
Components | Leucine--tRNA ligase | |||||||||
Keywords | RNA BINDING PROTEIN/INHIBITOR / Leucyl-tRNA Synthetase / Pneumonia / RNA BINDING PROTEIN-INHIBITOR complex | |||||||||
Function / homology | Function and homology information leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Streptococcus pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Liu, R.J. / Li, H. / Wang, E.D. / Zhou, H. | |||||||||
Funding support | China, 2items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2021 Title: Discovery of benzhydrol-oxaborole derivatives as Streptococcus pneumoniae leucyl-tRNA synthetase inhibitors. Authors: Hao, G. / Li, H. / Yang, F. / Dong, D. / Li, Z. / Ding, Y. / Pan, W. / Wang, E. / Liu, R. / Zhou, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bzj.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bzj.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 7bzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bzj_validation.pdf.gz | 816.6 KB | Display | wwPDB validaton report |
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Full document | 7bzj_full_validation.pdf.gz | 818.8 KB | Display | |
Data in XML | 7bzj_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 7bzj_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/7bzj ftp://data.pdbj.org/pub/pdb/validation_reports/bz/7bzj | HTTPS FTP |
-Related structure data
Related structure data | 4k48S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21091.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC 700669 / Spain 23F-1) (bacteria) Strain: ATCC 700669 / Spain 23F-1 / Gene: leuS, SPN23F02440 / Production host: Escherichia coli (E. coli) / References: UniProt: B8ZKS5, leucine-tRNA ligase |
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#2: Chemical | ChemComp-FGX / [( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.26 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris (pH5.5), 2.1M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 18, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 21319 / % possible obs: 100 % / Redundancy: 34.2 % / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.033 / Rrim(I) all: 0.199 / Χ2: 0.978 / Net I/σ(I): 4.3 / Num. measured all: 728749 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4K48 Resolution: 2→31.4 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.85 Å2 / Biso mean: 29.2203 Å2 / Biso min: 13.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→31.4 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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