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Yorodumi- PDB-6wq6: Xanthomonas citri Methionyl-tRNA synthetase in complex with methionine -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wq6 | |||||||||||||||
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Title | Xanthomonas citri Methionyl-tRNA synthetase in complex with methionine | |||||||||||||||
Components | Methionine--tRNA ligase | |||||||||||||||
Keywords | LIGASE / Substrate / Complex / tRNA / aminoacylation | |||||||||||||||
Function / homology | Function and homology information methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA binding / ATP binding / metal ion binding / cytosol Similarity search - Function | |||||||||||||||
Biological species | Xanthomonas citri (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | |||||||||||||||
Authors | Mercaldi, G.F. / Benedetti, C.E. | |||||||||||||||
Funding support | Brazil, 4items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Molecular basis for diaryldiamine selectivity and competition with tRNA in a type 2 methionyl-tRNA synthetase from a Gram-negative bacterium. Authors: Mercaldi, G.F. / Andrade, M.O. / Zanella, J.L. / Cordeiro, A.T. / Benedetti, C.E. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wq6.cif.gz | 132.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wq6.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 6wq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/6wq6 ftp://data.pdbj.org/pub/pdb/validation_reports/wq/6wq6 | HTTPS FTP |
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-Related structure data
Related structure data | 6wqiC 6wqsC 6wqtC 1pfyS 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
#1: Protein | Mass: 77436.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas citri (bacteria) / Strain: 306 / Gene: metG, metS, XAC1386 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8PMP0, methionine-tRNA ligase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MET / |
#4: 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: 1.98 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl, 28 - 32 % PEG 4000, 0.2 M MgCl2 / PH range: 7.9-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 24, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→47.63 Å / Num. obs: 68460 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 1 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.022 / Rrim(I) all: 0.079 / Net I/σ(I): 19.2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PFY Resolution: 1.7→47.63 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.722 / SU ML: 0.11 / SU R Cruickshank DPI: 0.1046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.106 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.65 Å2 / Biso mean: 34.267 Å2 / Biso min: 19.92 Å2
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Refinement step | Cycle: final / Resolution: 1.7→47.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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