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Yorodumi- PDB-6hb7: Crystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hb7 | ||||||||||||
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Title | Crystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyrosyl)sulfamoyl-N3-methyluridine | ||||||||||||
Components | Tyrosine--tRNA ligase | ||||||||||||
Keywords | LIGASE / protein-inhibitor complex / Rossmann fold / 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 / molecular replacement / Resolution: 1.9 Å | ||||||||||||
Authors | De Graef, S. / Pang, L. / Strelkov, S.V. / Weeks, S.D. | ||||||||||||
Funding support | Belgium, 3items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2019 Title: Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases. Authors: Nautiyal, M. / De Graef, S. / Pang, L. / Gadakh, B. / 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 | 6hb7.cif.gz | 346.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hb7.ent.gz | 279.1 KB | Display | PDB format |
PDBx/mmJSON format | 6hb7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hb7_validation.pdf.gz | 969.7 KB | Display | wwPDB validaton report |
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Full document | 6hb7_full_validation.pdf.gz | 973.9 KB | Display | |
Data in XML | 6hb7_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 6hb7_validation.cif.gz | 53.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/6hb7 ftp://data.pdbj.org/pub/pdb/validation_reports/hb/6hb7 | HTTPS FTP |
-Related structure data
Related structure data | 6hb5C 6hb6C 6i5yC 6q89C 6q8aC 6q8bC 6q8cC C: citing same article (ref.) |
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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) / 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: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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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: 49.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / 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 (1M stock solution adjusted to pH 6), 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 (1M stock solution adjusted to pH 6), 20% (v/v) ethylene glycol For soaking crystals were transferred to drop containing mother liquor supplemented with 2 mM inhibitor. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2017 | ||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.86→88.03 Å / Num. obs: 76335 / % possible obs: 98.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.11 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.061 / Rrim(I) all: 0.113 / Net I/σ(I): 9 / Num. measured all: 272521 / Scaling rejects: 2043 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.85 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.142 / SU Rfree Cruickshank DPI: 0.141
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Displacement parameters | Biso max: 128.78 Å2 / Biso mean: 39.51 Å2 / Biso min: 15.34 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→27.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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