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Yorodumi- PDB-5xet: Crystal structure of Mycobacterium tuberculosis methionyl-tRNA sy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xet | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis methionyl-tRNA synthetase bound by methionyl-adenylate (Met-AMP) | ||||||
Components | Methionine--tRNA ligase | ||||||
Keywords | LIGASE / synthetase / aminoacyl-tRNA synthetase / complex / ATP | ||||||
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 H37Ra (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Wang, W. / Qin, B. / Wojdyla, J.A. / Wang, M. / Gao, X. / 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 | 5xet.cif.gz | 199.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xet.ent.gz | 157.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xet.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xet_validation.pdf.gz | 736.8 KB | Display | wwPDB validaton report |
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Full document | 5xet_full_validation.pdf.gz | 742.6 KB | Display | |
Data in XML | 5xet_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 5xet_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/5xet ftp://data.pdbj.org/pub/pdb/validation_reports/xe/5xet | HTTPS FTP |
-Related structure data
Related structure data | 5xgqC 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: 59419.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria) Strain: ATCC 25177 / H37Ra / Gene: metG, MRA_1016 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A5U150, methionine-tRNA ligase | ||
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#2: Chemical | ChemComp-ME8 / [[( | ||
#3: Chemical | ChemComp-EDO / | ||
#4: Chemical | ChemComp-MG / #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: 2.49 Å3/Da / Density % sol: 50.54 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.9 Details: 0.2M Lithium sulfate monohydrate, 19% PEG 3350, bis tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→37.42 Å / Num. obs: 49191 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 45.55 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.156 / Net I/σ(I): 4.77 |
Reflection shell | Resolution: 2.38→2.54 Å / Redundancy: 2.13 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 8103 / CC1/2: 0.68 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2x1l Resolution: 2.38→37.42 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27.08 Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→37.42 Å
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Refine LS restraints |
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LS refinement shell |
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