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Yorodumi- PDB-6wrk: Crystal structure of 3rd-generation Mj 3-nitro-tyrosine tRNA synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wrk | ||||||||||||
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Title | Crystal structure of 3rd-generation Mj 3-nitro-tyrosine tRNA synthetase ("A7") bound to 3-nitro-tyrosine | ||||||||||||
Components | Tyrosine--tRNA ligase | ||||||||||||
Keywords | LIGASE / aminoacyl-tRNA synthetase / 3-nitro-tyrosine | ||||||||||||
Function / homology | Function and homology information tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||||||||
Authors | Beyer, J.N. / Hosseinzadeh, P. / Karplus, P.A. / Mehl, R.A. / Cooley, R.B. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Mol.Biol. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wrk.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wrk.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 6wrk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/6wrk ftp://data.pdbj.org/pub/pdb/validation_reports/wr/6wrk | HTTPS FTP |
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-Related structure data
Related structure data | 6wrnC 6wrqC 6wrtC 4ndaS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36136.898 Da / Num. of mol.: 1 / Mutation: Y32H, H70T, D158H, I159A, L162R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: tyrS, MJ0389 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q57834, tyrosine-tRNA ligase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.66 % |
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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 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2019 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45.36 Å / Num. obs: 28169 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.998 / Net I/σ(I): 10.17 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 7238 / CC1/2: 0.31 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NDA Resolution: 1.95→45.36 Å / SU ML: 0.2811 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.527 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: 43.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→45.36 Å
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Refine LS restraints |
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LS refinement shell |
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