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Yorodumi- PDB-6hhy: Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hhy | ||||||||||||
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Title | Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine | ||||||||||||
Components | Serine--tRNA ligase | ||||||||||||
Keywords | LIGASE / Coil-coil / Beta barrel / tRNA synthetase / Inhibitor / Complex | ||||||||||||
Function / homology | Function and homology information selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||||||||
Authors | Pang, L. / De Graef, S. / Weeks, S.D. / Strelkov, S.V. | ||||||||||||
Funding support | Belgium, 3items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases. Authors: Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Zorzini, V. / Economou, A. / Strelkov, S.V. / Van Aerschot, A. / Weeks, S.D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hhy.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hhy.ent.gz | 143.5 KB | Display | PDB format |
PDBx/mmJSON format | 6hhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/6hhy ftp://data.pdbj.org/pub/pdb/validation_reports/hh/6hhy | HTTPS FTP |
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-Related structure data
Related structure data | 6hdzC 6he1C 6he3C 6hhvC 6hhwC 6hhxC 6hhzC 6hi0C 6rltC 6rluC 6rlvC 6s30C 6sjcC 2dq3S 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: 48669.180 Da / Num. of mol.: 1 / Fragment: Seryl-tRNA synthetase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: serS, AGG09_05015, B1727_25560, B4U21_07300, B4U22_08075, BB785_18280, BL124_0015080, BN49_2024, C3483_17160, C3F39_05595, C9J88_18700, CPT10_05250, CSC88_02630, CWQ24_18365, PMK1_03261, SM57_00973 Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS References: UniProt: W9BNU9, UniProt: A6T6Z0*PLUS, serine-tRNA ligase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FZT / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM DTT, was mixed with an equal volume of 7.5% w/v PEG 8000, 50 mM CaCl2, 20% v/v ethylene glycol, 100 mM Morpheus ...Details: Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM DTT, was mixed with an equal volume of 7.5% w/v PEG 8000, 50 mM CaCl2, 20% v/v ethylene glycol, 100 mM Morpheus buffer system 1 (MES/Imidazole) pH 6.5. Suitable crystals were soaked with 2 mM compound in a similar crystallization solution containing a 10% w/v PEG 8000. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.972422 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.98→76.14 Å / Num. obs: 57726 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 57.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.03 / Rrim(I) all: 0.089 / Net I/σ(I): 12.1 / Num. measured all: 497991 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model generated from structure 2DQ3 Resolution: 2.27→67.52 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.151
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Displacement parameters | Biso max: 168.94 Å2 / Biso mean: 60.09 Å2 / Biso min: 35.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.27→67.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Origin x: -11.5872 Å / Origin y: -31.0369 Å / Origin z: -9.7036 Å
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Refinement TLS group | Selection details: {A|*} |