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Yorodumi- PDB-1mkh: C-terminal domain of methionyl-tRNA synthetase from Pyrococcus abyssi -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mkh | ||||||
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Title | C-terminal domain of methionyl-tRNA synthetase from Pyrococcus abyssi | ||||||
Components | C-terminal domain of Methionyl-tRNA synthetase | ||||||
Keywords | LIGASE / beta barrel / dimerization domain | ||||||
Function / homology | Function and homology information methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Crepin, T. / Schmitt, E. / Blanquet, S. / Mechulam, Y. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structure and function of the C-terminal domain of methionyl-tRNA synthetase Authors: Crepin, T. / Schmitt, E. / Blanquet, S. / Mechulam, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mkh.cif.gz | 30.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mkh.ent.gz | 21.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/1mkh ftp://data.pdbj.org/pub/pdb/validation_reports/mk/1mkh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12062.238 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 616-722 of SWS Q9V011 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: metG / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9V011, methionine-tRNA ligase |
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#2: 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: 2.84 Å3/Da / Density % sol: 56.69 % | |||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: peg 8000, potassium phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP at 297K | |||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 7, 2000 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→25.6 Å / Num. all: 9605 / Num. obs: 9605 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 46.5 Å2 / Rsym value: 0.052 |
Reflection shell | Resolution: 2.01→2.06 Å / Redundancy: 1.9 % / Num. unique all: 529 / Rsym value: 0.208 / % possible all: 75.9 |
Reflection | *PLUS Num. obs: 9286 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 75.9 % / Rmerge(I) obs: 0.208 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→15 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.54 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→15 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.289 / Rfactor Rwork: 0.275 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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