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Yorodumi- PDB-7ap3: Crystal structure of E. coli tyrosyl-tRNA synthetase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ap3 | ||||||
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Title | Crystal structure of E. coli tyrosyl-tRNA synthetase in complex with TyrS7HMDDA | ||||||
Components | Tyrosine--tRNA ligase | ||||||
Keywords | LIGASE / protein-inhibitor complex / tRNA aminoacylation | ||||||
Function / homology | Function and homology information tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / protein homodimerization activity / RNA binding / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | De Graef, S. / Pang, L. / Strelkov, S.V. / Weeks, S.D. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Molecules / Year: 2020 Title: Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors. Authors: Zhang, B. / Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Lescrinier, E. / Rozenski, J. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ap3.cif.gz | 344.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ap3.ent.gz | 277.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ap3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/7ap3 ftp://data.pdbj.org/pub/pdb/validation_reports/ap/7ap3 | HTTPS FTP |
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-Related structure data
Related structure data | 7ap1C 7ap2C 7ap4C 4oudS C: citing same article (ref.) 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
#1: Protein | Mass: 47594.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Strain: DE3 / Gene: tyrS, ECBD_2006 / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS References: UniProt: A0A140NBN7, UniProt: P0AGJ9*PLUS, tyrosine-tRNA ligase #2: Chemical | #3: Chemical | #4: 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: 2.51 Å3/Da / Density % sol: 50.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: Holo enzyme crystals were grown in 0.1 M BIS-TRIS pH 6.5, 10-15% PEG 3350, 20 mM glutamate pH 6 (1M stock solution adjusted to pH 5) and 20% (v/v) ethylene glycol. For soaking crystals were ...Details: Holo enzyme crystals were grown in 0.1 M BIS-TRIS pH 6.5, 10-15% PEG 3350, 20 mM glutamate pH 6 (1M stock solution adjusted to pH 5) and 20% (v/v) ethylene glycol. For soaking crystals were transferred to a drop containing mother liquor supplemented with 2 mM inhibitor. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.968625 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.968625 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.998→65.12 Å / Num. obs: 63743 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 29.52 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.065 / Rrim(I) all: 0.126 / Net I/σ(I): 7.4 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.5 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OUD Resolution: 2→54.681 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.25 / 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: 120.77 Å2 / Biso mean: 41.4637 Å2 / Biso min: 16.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→54.681 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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