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Yorodumi- PDB-6spo: Structure of the Escherichia coli methionyl-tRNA synthetase compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6spo | ||||||
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Title | Structure of the Escherichia coli methionyl-tRNA synthetase complexed with methionine | ||||||
Components | Methionine--tRNA ligase | ||||||
Keywords | TRANSLATION / tRNA aminoacylation | ||||||
Function / homology | Function and homology information methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / protein homodimerization activity / zinc ion binding / ATP binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Nigro, G. / Schmitt, E. / Mechulam, Y. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2020 Title: Use of beta3-methionine as an amino acid substrate of Escherichia coli methionyl-tRNA synthetase. Authors: Nigro, G. / Bourcier, S. / Lazennec-Schurdevin, C. / Schmitt, E. / Marliere, P. / Mechulam, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6spo.cif.gz | 453.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6spo.ent.gz | 307.7 KB | Display | PDB format |
PDBx/mmJSON format | 6spo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/6spo ftp://data.pdbj.org/pub/pdb/validation_reports/sp/6spo | HTTPS FTP |
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-Related structure data
Related structure data | 6spnC 6sppC 6spqC 6sprC 1qqtS S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 64730.008 Da / Num. of mol.: 1 / Mutation: Truncated after residue 547; His-tagged Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: metG, BvCmsKSP058_01266, BvCmsNSP007_01600, ED648_21370, UN91_27160 Production host: Escherichia coli (E. coli) References: UniProt: A0A0F3U9S7, UniProt: P00959*PLUS, methionine-tRNA ligase |
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-Non-polymers , 5 types, 752 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-CIT / | ||||
#4: Chemical | #5: Chemical | ChemComp-MET / | #6: Water | ChemComp-HOH / | |
-Details
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: 2.33 Å3/Da / Density % sol: 47.28 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion / pH: 7 Details: 1.08 M ammonium citrate, 10 mM potassium phosphate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2018 |
Radiation | Monochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→33.1 Å / Num. obs: 178894 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.44 Å2 / CC1/2: 0.998 / Rsym value: 0.105 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.2→1.27 Å / Mean I/σ(I) obs: 1.11 / Num. unique obs: 29243 / CC1/2: 0.326 / Rsym value: 1.638 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QQT Resolution: 1.2→33.05 Å / SU ML: 0.1557 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.1559 Details: Refinement was performed using explicit riding hydrogen atoms generated in phenix.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→33.05 Å
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Refine LS restraints |
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LS refinement shell |
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