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- PDB-6wrt: Crystal structure of Mj 3-nitro-tyrosine tRNA synthetase (5B) C70... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wrt | ||||||||||||
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Title | Crystal structure of Mj 3-nitro-tyrosine tRNA synthetase (5B) C70A/S158C variant bound to 3-nitro-tyrosine | ||||||||||||
![]() | Tyrosine--tRNA ligase | ||||||||||||
![]() | LIGASE / aminoacyl-tRNA synthetase / 3-nitro-tyrosine | ||||||||||||
Function / homology | ![]() tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Beyer, J.N. / Hosseinzadeh, P. / Karplus, P.A. / Mehl, R.A. / Cooley, R.B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Overcoming Near-Cognate Suppression in a Release Factor 1-Deficient Host with an Improved Nitro-Tyrosine tRNA Synthetase. Authors: Beyer, J.N. / Hosseinzadeh, P. / Gottfried-Lee, I. / Van Fossen, E.M. / Zhu, P. / Bednar, R.M. / Karplus, P.A. / Mehl, R.A. / Cooley, R.B. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.1 KB | Display | ![]() |
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PDB format | ![]() | 114.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wrkC ![]() 6wrnC ![]() 6wrqC ![]() 4ndaS C: citing same article ( 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 36071.867 Da / Num. of mol.: 1 / Mutation: Y32H, H70A,D158C, I159A, L162R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: tyrS, MJ0389 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 22-23% PEG 300, 5% PEG 8000, 10% glycerol and 100 mM Tris pH 7.9 to 8.2 PH range: 7.9-8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Si / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→45.52 Å / Num. obs: 55943 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 13.12 |
Reflection shell | Resolution: 1.55→1.65 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 0.96 / Num. unique obs: 17809 / CC1/2: 0.415 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NDA Resolution: 1.55→45.52 Å / SU ML: 0.2109 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.0981 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→45.52 Å
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Refine LS restraints |
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LS refinement shell |
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