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Yorodumi- PDB-5u36: Crystal Structure Of A Mutant M. Jannashii Tyrosyl-tRNA Synthetase -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u36 | ||||||
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Title | Crystal Structure Of A Mutant M. Jannashii Tyrosyl-tRNA Synthetase | ||||||
Components | Tyrosine--tRNA ligase | ||||||
Keywords | LIGASE / tyrosine phosphorylation | ||||||
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: 3.03 Å | ||||||
Authors | Luo, X. / Fu, G. / Zhu, X. / Wilson, I.A. / Wang, F. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Genetically encoding phosphotyrosine and its nonhydrolyzable analog in bacteria. Authors: Luo, X. / Fu, G. / Wang, R.E. / Zhu, X. / Zambaldo, C. / Liu, R. / Liu, T. / Lyu, X. / Du, J. / Xuan, W. / Yao, A. / Reed, S.A. / Kang, M. / Zhang, Y. / Guo, H. / Huang, C. / Yang, P.Y. / ...Authors: Luo, X. / Fu, G. / Wang, R.E. / Zhu, X. / Zambaldo, C. / Liu, R. / Liu, T. / Lyu, X. / Du, J. / Xuan, W. / Yao, A. / Reed, S.A. / Kang, M. / Zhang, Y. / Guo, H. / Huang, C. / Yang, P.Y. / Wilson, I.A. / Schultz, P.G. / Wang, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u36.cif.gz | 127.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u36.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 5u36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/5u36 ftp://data.pdbj.org/pub/pdb/validation_reports/u3/5u36 | HTTPS FTP |
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-Related structure data
Related structure data | 4pbrS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 2 - 307 / Label seq-ID: 2 - 307
NCS ensembles : (Details: 1 ) |
-Components
#1: Protein | Mass: 36005.789 Da / Num. of mol.: 2 / Mutation: Y32S, L65A, F108K, Q109H, D158G, L162K 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(DE3) / References: UniProt: Q57834, tyrosine-tRNA ligase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 15-25% PEG3350, 50 mM sodium cacodylate trihydrate, pH 6.0-7.0 PH range: 6.0 - 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.03→65.28 Å / Num. obs: 15184 / % possible obs: 98.1 % / Redundancy: 3.6 % / CC1/2: 1 / Rsym value: 0.088 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 3.05→3.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.55 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PBR Resolution: 3.03→65.28 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.889 / SU B: 21.426 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.897 Å2
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Refinement step | Cycle: 1 / Resolution: 3.03→65.28 Å
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Refine LS restraints |
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