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- PDB-3vu8: Metionyl-tRNA synthetase from Thermus thermophilus complexed with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vu8 | ||||||
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Title | Metionyl-tRNA synthetase from Thermus thermophilus complexed with methionyl-adenylate analogue | ||||||
![]() | Methionine--tRNA ligase | ||||||
![]() | LIGASE / protein Met-AMP complex | ||||||
Function / homology | ![]() methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Konno, M. / Kato-Murayama, M. / Toma-Fukai, S. / Uchikawa, E. / Nureki, O. / Yokoyama, S. | ||||||
![]() | ![]() Title: The modeling of structures of specific conformation of homosysteine-AMP leading to thiolactone-formation on class Ia aminoacyl-tRNA synthetases Authors: Konno, M. / Kato-Murayama, M. / Takeda, R. / Takasaka, R. / Uchikawa, E. / Toma-Fukai, S. / Ishii, R. / Nureki, O. / Yokoyama, S. #1: ![]() Title: The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules Authors: Sugiura, I. / Nureki, O. / Ugaji-Yoshikawa, Y. / Kuwabara, S. / Shimada, A. / Tateno, M. / Lorber, B. / Giege, R. / Moras, D. / Yokoyama, S. / Konno, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.6 KB | Display | ![]() |
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PDB format | ![]() | 89.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1a8hS S: Starting model for refinement |
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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: 58220.645 Da / Num. of mol.: 1 / Fragment: UNP residues 1-502 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MDS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG6000, DTT, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 14, 1999 / Details: mirrors |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 23727 / Num. obs: 23727 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.05 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 7.69 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 1.7 / Num. unique all: 911 / % possible all: 70.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A8H Resolution: 2.2→8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.7 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å
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