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- PDB-3h97: Structure of a mutant methionyl-tRNA synthetase with modified spe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h97 | ||||||
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Title | Structure of a mutant methionyl-tRNA synthetase with modified specificity | ||||||
![]() | Methionyl-tRNA synthetase | ||||||
![]() | LIGASE / Rossmann fold / Aminoacyl-tRNA synthetase / ATP-binding / Metal-binding / Nucleotide-binding / Protein biosynthesis / RNA-binding / tRNA-binding | ||||||
Function / homology | ![]() methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA binding / protein homodimerization activity / zinc ion binding / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schmitt, E. / Tanrikulu, I.C. / Yoo, T.H. / Panvert, M. / Tirrell, D.A. / Mechulam, Y. | ||||||
![]() | ![]() Title: Switching from an induced-fit to a lock-and-key mechanism in an aminoacyl-tRNA synthetase with modified specificity. Authors: Schmitt, E. / Tanrikulu, I.C. / Yoo, T.H. / Panvert, M. / Tirrell, D.A. / Mechulam, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.4 KB | Display | ![]() |
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PDB format | ![]() | 110.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.2 KB | Display | ![]() |
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Full document | ![]() | 436.4 KB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 49.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3h99C ![]() 3h9bC ![]() 3h9cC ![]() 1qqtS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 63907.199 Da / Num. of mol.: 1 / Fragment: M547 domain: UNP residues 2-548 / Mutation: L13S, Y260L, H301L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.21 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: Ammonium citrate, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2007 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 59541 / Num. obs: 59541 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 2.54 % / Biso Wilson estimate: 15.76 Å2 / Rmerge(I) obs: 0.023 / Rsym value: 0.022 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.042 / Num. unique obs: 9580 / Rsym value: 0.038 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1QQT Resolution: 1.7→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.911 / σ(F): 0
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Solvent computation | Bsol: 43.011 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.15 Å2 / Biso mean: 11.017 Å2 / Biso min: 1.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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Xplor file |
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