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Yorodumi- PDB-4oud: Engineered tyrosyl-tRNA synthetase with the nonstandard amino aci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oud | ||||||
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Title | Engineered tyrosyl-tRNA synthetase with the nonstandard amino acid L-4,4-biphenylalanine | ||||||
Components | (Tyrosyl-tRNA synthetase) x 2 | ||||||
Keywords | LIGASE / complex with L-tyrosine / Rossmann fold / tRNA | ||||||
Function / homology | Function and homology information tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Takeuchi, R. / Mandell, D.J. / Lajoie, M.J. / Church, G.M. / Stoddard, B.L. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Biocontainment of genetically modified organisms by synthetic protein design. Authors: Mandell, D.J. / Lajoie, M.J. / Mee, M.T. / Takeuchi, R. / Kuznetsov, G. / Norville, J.E. / Gregg, C.J. / Stoddard, B.L. / Church, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oud.cif.gz | 307.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oud.ent.gz | 250.9 KB | Display | PDB format |
PDBx/mmJSON format | 4oud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oud_validation.pdf.gz | 465.1 KB | Display | wwPDB validaton report |
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Full document | 4oud_full_validation.pdf.gz | 479.8 KB | Display | |
Data in XML | 4oud_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 4oud_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/4oud ftp://data.pdbj.org/pub/pdb/validation_reports/ou/4oud | HTTPS FTP |
-Related structure data
Related structure data | 2yxnS 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
#1: Protein | Mass: 47399.477 Da / Num. of mol.: 1 / Mutation: L49A, F236A, W260A, T263A, F271W, F275G, L303BIF Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MC4100 / Gene: tyrS, BN896_1452 / Production host: Escherichia coli (E. coli) References: UniProt: U6N9P2, UniProt: A0A0H2UKY9*PLUS, tyrosine-tRNA ligase |
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#2: Protein | Mass: 43530.457 Da / Num. of mol.: 1 / Mutation: L49A, F236A, W260A, T263A, F271W, F275G, L303BIF Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MC4100 / Gene: tyrS, BN896_1452 / Production host: Escherichia coli (E. coli) References: UniProt: U6N9P2, UniProt: A0A0H2UKZ0*PLUS, tyrosine-tRNA ligase |
#3: Chemical | ChemComp-TYR / |
#4: Water | ChemComp-HOH / |
Sequence details | RESIDUES 355 THROUGH 402 ARE MISSING IN THE COORDINATES OF CHAIN B. HOWEVER THE AUTHORS SEE THE ...RESIDUES 355 THROUGH 402 ARE MISSING IN THE COORDINATE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M sodium malonate, 18 % PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å |
Detector | Detector: CCD / Date: Dec 12, 2013 |
Radiation | Monochromator: Si 220 asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. all: 27201 / Num. obs: 26929 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.65 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2YXN Resolution: 2.65→45 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.876 / SU B: 31.51 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 1.054 / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 58.281 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→45 Å
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Refine LS restraints |
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