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Yorodumi- PDB-5xgq: Crystal structure of apo form (free-state) Mycobacterium tubercul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xgq | ||||||
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Title | Crystal structure of apo form (free-state) Mycobacterium tuberculosis methionyl-tRNA synthetase | ||||||
Components | Methionine-tRNA ligaseMethionine—tRNA ligase | ||||||
Keywords | LIGASE / Methionyl-tRNA Synthetase / Protein translation / Mycobacterium tuberculosis / Anticodon-binding domain of tRNA | ||||||
Function / homology | Function and homology information methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å | ||||||
Authors | Wang, W. / Wang, M. / Wojdyla, J.A. / Cui, S. | ||||||
Citation | Journal: IUCrJ / Year: 2018 Title: Structural characterization of free-state and product-stateMycobacterium tuberculosismethionyl-tRNA synthetase reveals an induced-fit ligand-recognition mechanism Authors: Wang, W. / Qin, B. / Wojdyla, J.A. / Wang, M. / Gao, X. / Cui, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xgq.cif.gz | 237.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xgq.ent.gz | 187.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/5xgq ftp://data.pdbj.org/pub/pdb/validation_reports/xg/5xgq | HTTPS FTP |
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-Related structure data
Related structure data | 5xetC 2x1lS 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: 60248.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria) Strain: ATCC 25177 / H37Ra / Gene: metG, MRA_1016 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3)pLysS AG / References: UniProt: A5U150, methionine-tRNA ligase #2: 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: 2.31 Å3/Da / Density % sol: 46.75 % / Description: plates |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.1 Details: 0.1M calcium acetate, 0.1M sodium cacodylate, 16%PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: AREA DETECTOR / Date: Aug 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.899→48.686 Å / Num. obs: 158725 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 1.68 % / Biso Wilson estimate: 28.233 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.094 / Χ2: 0.97 / Net I/σ(I): 6.68 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 1.53 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 27608 / CC1/2: 0.586 / Χ2: 0.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2x1l Resolution: 1.899→48.686 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 26.15 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.899→48.686 Å
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Refine LS restraints |
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LS refinement shell |
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